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Read alignment software tools | Whole-genome sequencing data analysis

An ubiquitous and fundamental step in high-throughput sequencing analysis is the alignment (mapping) of the generated reads to a reference sequence. To accomplish this task, numerous software tools have been proposed.Source text:(Fonseca et al.,…
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Bowtie
Desktop

Bowtie

A short read aligner that aligns short DNA sequences (reads) to the human…

A short read aligner that aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its…

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BWA
Desktop

BWA Burrows-Wheeler Aligner

Maps low-divergent sequences against a large reference genome, such as the…

Maps low-divergent sequences against a large reference genome, such as the human genome. BWA consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for…

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CORA
Desktop

CORA COmpressive Readmapping Accelerator

Achieves substantial runtime improvement through the use of compressive…

Achieves substantial runtime improvement through the use of compressive representation of the reads and a comprehensive homology map of the reference genome, when plugged into existing mapping tools.…

BLAST
Web
Desktop

BLAST Basic Local Alignment Search Tool

Allows to align query sequences against those present in a selected target…

Allows to align query sequences against those present in a selected target database. BLAST is a suite of programs, provided by NCBI, which can be used to quickly search a sequence database for…

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BLASTX
Web

BLASTX Translated BLAST: blastx

Searches protein database using a translated nucleotide query. BLASTX is a…

Searches protein database using a translated nucleotide query. BLASTX is a BLAST search application that compares the six-frame conceptual translation products of a nucleotide query sequence (both…

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BLAT
Desktop
Web

BLAT BLAST-Like Alignment Tool

Finds genomic sequences that match a protein or DNA sequence submitted by the…

Finds genomic sequences that match a protein or DNA sequence submitted by the user. BLAT is a very fast sequence alignment tool similar to BLAST typically used for searching similar sequences within…

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mrFAST/mrsFAST
Desktop

mrFAST/mrsFAST

They are designed to map short reads generated with the Illumina platform to…

They are designed to map short reads generated with the Illumina platform to reference genome assemblies; in a fast and memory-efficient manner.

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MAQ
Desktop

MAQ Mapping and Assembly with Quality

Builds mapping assemblies from short reads generated by the next-generation…

Builds mapping assemblies from short reads generated by the next-generation sequencing machines. Maq is particularly designed for Illumina-Solexa 1G Genetic Analyzer, and has preliminary functions to…

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Nanopolish
Desktop

Nanopolish

Provides a nanopore consensus algorithm using a signal-level hidden Markov…

Provides a nanopore consensus algorithm using a signal-level hidden Markov model (HMM). The main subprograms of Nanopolish are: (i) nanopolish extract which extracts reads in FASTA or FASTQ format…

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SOAP
Desktop

SOAP Short Oligonucleotide Analysis Package

A GPU-based software for aligning short reads with a reference sequence. SOAP…

A GPU-based software for aligning short reads with a reference sequence. SOAP can find all alignments with k mismatches, where k is chosen from 0 to 3. When aligning length-100 reads with the human…

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Segemehl
Desktop

Segemehl

Maps short sequencer reads to reference genomes. Segemehl is a read aligner…

Maps short sequencer reads to reference genomes. Segemehl is a read aligner that allows to detect mismatches, insertions and deletions. The software implements a matching strategy based on enhanced…

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Anfo
Desktop

Anfo

A mapper in the spirit of Soap/Maq/Bowtie, but its implementation takes more…

A mapper in the spirit of Soap/Maq/Bowtie, but its implementation takes more after BLAST/BLAT. Anfo is most useful for the alignment of sequencing reads where the DNA sequence is somehow modified…

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MIA
Desktop

MIA Mapping Iterative Assembler

The basic idea of this program is to align DNA sequencing fragments (shotgun or…

The basic idea of this program is to align DNA sequencing fragments (shotgun or targeted resequencing) to a reference, then call a consensus. Then the consensus is used as new reference and the…

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EAGER
Desktop

EAGER

Permits next-generation sequencing (NGS) analysis to reconstruct ancient…

Permits next-generation sequencing (NGS) analysis to reconstruct ancient genomes. EAGER is able to perform several raw read pre-processing steps, including the initial analysis of raw sequencing…

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marginAlign
Desktop

marginAlign

The package can be used to align reads to a reference genome and call single…

The package can be used to align reads to a reference genome and call single nucleotide variations (SNVs). It is specifically tailored for Oxford Nanopore Reads. The package comes with two programs:…

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SSAHA
Desktop

SSAHA Sequence Search and Alignment by Hashing Algorithm

A pairwise sequence alignment program designed for the efficient mapping of…

A pairwise sequence alignment program designed for the efficient mapping of sequencing reads onto genomic reference sequences. SSAHA reads of most sequencing platforms (ABI-Sanger, Roche 454,…

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Stampy
Desktop

Stampy

A package for the mapping of short reads from illumina sequencing machines onto…

A package for the mapping of short reads from illumina sequencing machines onto a reference genome.

BLASTN
Web

BLASTN Standard Nucleotide BLAST

Programs search nucleotide databases using a nucleotide query. BLASTN key…

Programs search nucleotide databases using a nucleotide query. BLASTN key features are searching with short sequencing and cross-species comparison.

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PBSuite
Desktop

PBSuite

Affords a way for analysis of Pacific Biosciences long-read sequencing data.…

Affords a way for analysis of Pacific Biosciences long-read sequencing data. PBSuite is composed of two projects: PBJelly and PBHoney. The first one is an automated pipeline for aligning long…

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SeqMap
Desktop

SeqMap

Maps large amount of oligonucleotide to the genome. SeqMap allows up to five…

Maps large amount of oligonucleotide to the genome. SeqMap allows up to five mixed substitutions and inserted/deleted (indel) nucleotides in the mapping, which is considered. The software also…

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SHRiMP
Desktop

SHRiMP SHort Read Mapping Program

Allows to align genomic reads against a target genome. SHRiMP primarily targets…

Allows to align genomic reads against a target genome. SHRiMP primarily targets mapping accuracy, enabling the alignment of reads with extensive polymorphism and sequencing errors. The software…

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CloudBurst
Desktop

CloudBurst

A parallel read-mapping algorithm optimized for mapping next-generation…

A parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP…

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RMAP
Desktop

RMAP

Reads maps from next-generation sequencing (NGS) technology. RMAP was developed…

Reads maps from next-generation sequencing (NGS) technology. RMAP was developed for mapping Illumina reads and has been used to map Roche/454 and ABI SOLiD reads. The software reads map with or…

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Subread
Desktop

Subread

A toolkit for processing next-gen sequencing data. These programs were also…

A toolkit for processing next-gen sequencing data. These programs were also implemented in Bioconductor R package Rsubread.

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PEAR
Desktop

PEAR

Produces merged raw Illumina paired-end reads with low false positive rates…

Produces merged raw Illumina paired-end reads with low false positive rates (FPRs). PEAR combines reads by maximizing the assembly score (AS) of the read overlap via a scoring matrix. It evaluates…

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GSNAP
Desktop

GSNAP

Aligns both single- and paired-end reads as short as 14 nt and of arbitrarily…

Aligns both single- and paired-end reads as short as 14 nt and of arbitrarily long length. GSNAP can detect short- and long-distance splicing, including interchromosomal splicing, in individual…

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NextGenMap
Desktop

NextGenMap

A read mapper that is more than twice as fast as BWA, while achieving a mapping…

A read mapper that is more than twice as fast as BWA, while achieving a mapping sensitivity similar to Stampy or Bowtie2. NextGenMap aligns reads reliably to a reference genome even when the sequence…

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PerM
Desktop

PerM Periodic Seed Mapping

Provides highly efficient mapping solutions for genome-scale mapping projects…

Provides highly efficient mapping solutions for genome-scale mapping projects involving Illumina or SOLiD data. The data structure in PerM requires only 4.5 bytes per base to index the human genome,…

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Isaac Genome…
Desktop

Isaac Genome Alignment Software

Aligns next-generation sequencing (NGS) data with low-error rates (single or…

Aligns next-generation sequencing (NGS) data with low-error rates (single or paired-ends). Isaac Genome Alignment Software has been designed to take full advantage of all the computational power…

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seq2HLA
Desktop

seq2HLA

A method for obtaining an individualXs HLA class I and II type and expression…

A method for obtaining an individualXs HLA class I and II type and expression using standard NGS RNA-Seq data. Because the algorithm uses standard RNA-Seq reads and requires no change to laboratory…

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HiLive
Desktop

HiLive

Implements a k-mer based alignment strategy. HiLive continuously reads…

Implements a k-mer based alignment strategy. HiLive continuously reads intermediate BCL files produced by Illumina sequencers and then extends initial k-mer matches by increasingly produced data from…

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diffsplicing
Desktop

diffsplicing

A method for ranking the genes and transcripts according to the temporal change…

A method for ranking the genes and transcripts according to the temporal change they show in their expression levels. In order to identify differential splicing and its underlying dynamics, we model…

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NanoOK
Desktop

NanoOK

Provides comprehensive alignment-based analysis of Nanopore reads through a…

Provides comprehensive alignment-based analysis of Nanopore reads through a simple, easy to use interface. NanoOK generates detailed tabular and graphical output plus an in-depth multi-page PDF…

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GraphMap
Desktop

GraphMap

Analyses nanopore sequencing reads. GraphMap progressively refines candidate…

Analyses nanopore sequencing reads. GraphMap progressively refines candidate alignments to robustly handle potentially high-error rates and a fast graph traversal to align long reads with speed and…

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SAPAS
Desktop

SAPAS

A pipeline for RNA-seq method to research polyA. SAPAS performs a systematic…

A pipeline for RNA-seq method to research polyA. SAPAS performs a systematic search and evaluation of protocols for typical steps to investigate to what extent these can indeed facilitate RNA-seq…

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MOSAIK
Desktop

MOSAIK

Maps next generation sequencing (NGS) reads to a reference genome. MOSAIK is a…

Maps next generation sequencing (NGS) reads to a reference genome. MOSAIK is a reference-guided aligner that uses a neural-network based training scheme and supports most existing sequencing…

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BFAST
Desktop

BFAST

Facilitates the fast and accurate mapping of short reads to reference…

Facilitates the fast and accurate mapping of short reads to reference sequences. BFAST can align the amount of data needed to fully resequence a human genome, one billion reads, with high sensitivity…

TEtools
Desktop

TEtools transposable elements tools

Provides analysis of TE expression. TEtools takes into account the TE sequence…

Provides analysis of TE expression. TEtools takes into account the TE sequence diversity of the genome. It can be applied to unannotated or unassembled genomes and is freely available under the GPL3.…

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mrsFAST
Desktop

mrsFAST Micro-read substitution-only Fast Alignment Search Tool

A fast, cache oblivious, SNP-aware aligner that can handle the multi-mapping of…

A fast, cache oblivious, SNP-aware aligner that can handle the multi-mapping of high throughput sequencing reads very efficiently. mrsFAST-Ultra improves mrsFAST, our first cache oblivious read…

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SparkBWA
Desktop

SparkBWA

Exploits the capabilities of a big data technology as Spark to boost the…

Exploits the capabilities of a big data technology as Spark to boost the performance of one of the most widely adopted aligner, the Burrows-Wheeler Aligner (BWA). The design of SparkBWA uses two…

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ISAS
Desktop

ISAS Imagenix Sequence Alignment System

Generates uniqueome data for human, mouse, worm and fly genomes in both…

Generates uniqueome data for human, mouse, worm and fly genomes in both color-space and nucleotide-space. ISAS permits to perform leading edge research without million Dollar compute farms. It is…

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SPRINT
Desktop

SPRINT SNP-free RNA editing IdeNtification Toolkit

Identifies RNA editing sites (RESs) by clustering single nucleotide variant…

Identifies RNA editing sites (RESs) by clustering single nucleotide variant (SNV) duplets, bypassing the need of single nucleotide polymorphism (SNP) annotations. SPRINT is applicable to any RNA-seq…

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ST Pipeline
Desktop

ST Pipeline

Permits to process and analyze the raw files generated with the Spatial…

Permits to process and analyze the raw files generated with the Spatial Transcriptomics (ST) method. ST Pipeline enables demultiplexing of spatially-resolved RNA-seq data and robust quality filtering…

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SpliceTrap
Desktop

SpliceTrap

A statistic tool for quantifying exon inclusion ratios in paired-end RNA-seq…

A statistic tool for quantifying exon inclusion ratios in paired-end RNA-seq data, with broad applications for the study of alternative splicing.

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Kart
Desktop

Kart

Provides a sequence aligner for sensitive and accurate mapping from…

Provides a sequence aligner for sensitive and accurate mapping from next-generation sequencing (NGS) reads to a reference genome. Kart uses both Burrorws-Wheeler transform (BWT) array and hash table.…

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LAMSA
Desktop

LAMSA Long Approximate Matches-based Split Aligner

Takes the advantage of the rareness of structural variants (SVs) to implement a…

Takes the advantage of the rareness of structural variants (SVs) to implement a specifically designed two-step read-splitting and alignment strategy. LAMSA initially splits the read into relatively…

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FBB
Desktop

FBB Fast Bayesian Bound

Compares RNA-seq alignment results across different algorithms. FBB uses…

Compares RNA-seq alignment results across different algorithms. FBB uses quality scores of the reads to align them to a genome of reference. Two theorems are provided to efficiently calculate the…

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GASSST
Desktop

GASSST Global Alignment Short Sequence Search Tool

Maps reads with mismatch and indel errors at a high speed. GASSST is a short…

Maps reads with mismatch and indel errors at a high speed. GASSST is a short read aligner that uses the seed and extend strategy. The software’s algorithm has three stages: (i) searching for exact…

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systemPipeR
Desktop

systemPipeR

An extensible environment for both building and running end-to-end analysis…

An extensible environment for both building and running end-to-end analysis workflows with automated report generation for a wide range of next-generation sequencing (NGS) applications. Its unique…

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Arioc
Desktop

Arioc

Identifies high-priority locations where potential alignments may be found.…

Identifies high-priority locations where potential alignments may be found. Arioc uses GPU-based parallel sort and reduction techniques. It consists of one-time-only initialization (memory…

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GNUMAP
Desktop

GNUMAP Genomic Next-generation Universal MAPper

A program designed to accurately map sequence data obtained from…

A program designed to accurately map sequence data obtained from next-generation sequencing machines (specifically that of Solexa/Illumina) back to a genome of any size.

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SEAL
Desktop

SEAL

A suite of distributed applications for aligning short DNA reads, and…

A suite of distributed applications for aligning short DNA reads, and manipulating and analyzing short read alignments.

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SePIA
Desktop

SePIA Sequence Processing Integration and Analysis

An open-source workflow introducing standardized processing and analysis of RNA…

An open-source workflow introducing standardized processing and analysis of RNA and small RNA data. SePIA provides ready execution for over 20 commonly known RNA-seq tools on top of an established…

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RazerS
Desktop

RazerS

A read mapping program with adjustable sensitivity based on counting q-grams.

A read mapping program with adjustable sensitivity based on counting q-grams.

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SplazerS
Desktop

SplazerS SplitRazerS

Serves to analyze sequences on biological data. SplazerS works about…

Serves to analyze sequences on biological data. SplazerS works about sensitivity for detecting large indel events particularly in variant-rich regions. This tool uses a more sensitive alignment…

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BarraCUDA
Desktop

BarraCUDA

Allows users to align large numbers of next generation DNA sequences. BarraCUDA…

Allows users to align large numbers of next generation DNA sequences. BarraCUDA uses the Burrows-Wheeler algorithm. This software aligns short noisy DNA sequences against one of the increasing number…

LAST
Web
Desktop

LAST

Enables fast and sensitive comparison of large sequences with arbitrarily…

Enables fast and sensitive comparison of large sequences with arbitrarily nonuniform composition. LAST can handle big sequence data, e.g: compare two vertebrate genomes and align billions of DNA…

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ERNE
Desktop

ERNE Extended Randomized Numerical alignEr

A short string alignment package whose goal is to provide an all-inclusive set…

A short string alignment package whose goal is to provide an all-inclusive set of tools to handle short (NGS-like) reads. ERNE 2 (a.k.a. bw-erne) uses the Burrows Wheeler Transformation (BWT) to…

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BatAlign
Desktop

BatAlign

An algorithm that integrated two strategies called ‘Reverse-alignment’ and…

An algorithm that integrated two strategies called ‘Reverse-alignment’ and ‘Deep-scan’ to improve the accuracy of read-alignment. BatAlign was able to obtain the highest F-measures in…

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CUSHAW
Desktop

CUSHAW

An open-source parallelized, sensitive and accurate short-read aligner for both…

An open-source parallelized, sensitive and accurate short-read aligner for both base-space and color-space sequences. This aligner is designed based on the well-known seed-and-extend heuristic and…

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PECaller
Desktop

PECaller

Allows to minimize the burden on networks and disk arrays. PECaller allows the…

Allows to minimize the burden on networks and disk arrays. PECaller allows the imposition of a population genetics-inspired prior on the data and the ability to fit sophisticated models of read…

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ParaBWT
Desktop

ParaBWT

Employs a progressive construction approach to incrementally build the…

Employs a progressive construction approach to incrementally build the Burrows-Wheeler transform (BWT) of a single genomic sequence segment-by-segment. ParaBWT is a practical parallel BWT and suffix…

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SHARAKU
Desktop

SHARAKU SHape Aligner of non-coding RNA developed by Keio University

Aligns two read mapping profiles of next-generation sequencing outputs for…

Aligns two read mapping profiles of next-generation sequencing outputs for non-coding RNAs. SHARAKU incorporates the primary and secondary sequence structures into an alignment of read mapping…

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SeqLib
Desktop

SeqLib

Provides a rapid and user-friendly interface to BAM/SAM/CRAM files, global…

Provides a rapid and user-friendly interface to BAM/SAM/CRAM files, global sequence alignment operations and sequence assembly. SeqLib provides a command-line tool for performing combinations of…

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Frame-Pro
Desktop

Frame-Pro

A profile homology search tool for PacBio reads. Frame-Pro is a tool using…

A profile homology search tool for PacBio reads. Frame-Pro is a tool using Hidden Markov Model (HMM) and directed acyclic graph to correct the errors in DNA sequencing reads. It can also provide…

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ntHash
Desktop

ntHash

A hashing algorithm tuned for processing DNA/RNA sequences. ntHash provides a…

A hashing algorithm tuned for processing DNA/RNA sequences. ntHash provides a fast way to compute multiple hash values for a given k-mer, without repeating the whole procedure for each value. To do…

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deBGA
Desktop

deBGA de Bruijn Graph-based Aligner

An innovative graph-based seed-and-extension algorithm to align high-throughput…

An innovative graph-based seed-and-extension algorithm to align high-throughput sequencing (HTS) reads to a reference genome that is organized and indexed using a de Bruijn graph. With its…

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OSS
Desktop

OSS Optimal Seed Solver

A dynamic-programming algorithm that finds the optimal seeds of a read, which…

A dynamic-programming algorithm that finds the optimal seeds of a read, which renders the minimum total seed frequency. Seed selection is an important step for pigeonhole based seed-and-extend read…

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rHAT
Desktop

rHAT regional Hashing-based Alignment Tool

A seed-and-extension-based read alignment approach specifically designed for…

A seed-and-extension-based read alignment approach specifically designed for noisy long reads. rHAT indexes reference genome by regional hash table (RHT), a hash table-based index which describes the…

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RNFtools
Desktop

RNFtools

An associate software package for Read Naming Format (RNF), a generic format…

An associate software package for Read Naming Format (RNF), a generic format for naming simulated next-generation sequencing reads. The format aims to remove dependency of evaluation tools of read…

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Halvade
Desktop

Halvade

Allows to execute DNA-seq/RNA-seq pipeline. Halvade is a Hadoop MapReduce…

Allows to execute DNA-seq/RNA-seq pipeline. Halvade is a Hadoop MapReduce implementation that enables sequencing pipelines to be executed in parallel on a multi-node and/or multi-core compute…

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HPG Aligner
Desktop

HPG Aligner

Upgrades the sensitivity and the rapidity of a DNA mapping by applying suffix…

Upgrades the sensitivity and the rapidity of a DNA mapping by applying suffix arrays. HPG aligner offers an optimal alternative to deal with long reads by reading directly the gzipped files, saving…

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Oqtans
Desktop

Oqtans Online quantitative transcriptome analysis

It is based on the Galaxy-framework and provides tools for read mapping,…

It is based on the Galaxy-framework and provides tools for read mapping, transcript reconstruction and quantitation as well as differential expression analysis.

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TRAP
Desktop
Web

TRAP Time-series RNA-seq Analysis Package

A comprehensive package integrating all necessary tasks such as mapping short…

A comprehensive package integrating all necessary tasks such as mapping short reads, measuring gene expression levels, finding differentially expressed genes (DEGs), clustering and pathway analysis…

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VarHMM
Desktop

VarHMM Variable-order paired HMM

Addresses higher order modeling issues and exploits similarities between reads…

Addresses higher order modeling issues and exploits similarities between reads to improve processing time. VarHMM is a variable order paired Hidden Markov Model (HMM) for sequence alignment and read…

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Meta-aligner
Desktop

Meta-aligner

Aligns long and very long reads to the reference genome very efficiently and…

Aligns long and very long reads to the reference genome very efficiently and accurately. Meta-aligner incorporates available short/long aligners as subcomponents and uses statistics from the…

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BWA-PSSM
Desktop

BWA-PSSM

A probabilistic short read aligner based on the use of position specific…

A probabilistic short read aligner based on the use of position specific scoring matrices (PSSM). Like many of the existing aligners it is fast and sensitive. Unlike most other aligners, however, it…

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SRmapper
Desktop

SRmapper

Determines the initial number of mismatches allowed and calculates alignment…

Determines the initial number of mismatches allowed and calculates alignment scores. SRmapper is a reference genome-hashing alignment tool that builds an alignment tool that was not restrictively…

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drFAST
Desktop

drFAST di-base read Fast Alignment Search Tool

It is designed to map di-base reads (SOLiD color space reads) to reference…

It is designed to map di-base reads (SOLiD color space reads) to reference genome assemblies.

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Oculus
Desktop

Oculus

Increases sequence alignment speed for redundant input. Oculus is a software…

Increases sequence alignment speed for redundant input. Oculus is a software package that attaches to standard aligners and exploits read redundancy by performing streaming compression, alignment,…

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DistMap
Desktop

DistMap

A user-friendly pipeline designed to map short reads in a MapReduce framework…

A user-friendly pipeline designed to map short reads in a MapReduce framework on a local Hadoop cluster.

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RAMICS
Desktop
Web

RAMICS Rapid Amplicon Mapping in Codon Space

A hidden Markov model reference mapper, designed to align coding and non-coding…

A hidden Markov model reference mapper, designed to align coding and non-coding DNA to a reference sequence. By default, RAMICS assumes DNA is coding and Sanger-sequenced. Options allow the user to…

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SureMap
Desktop

SureMap

Handles reads requiring special attention during read mapping. SureMap can map…

Handles reads requiring special attention during read mapping. SureMap can map short and long reads to a reference genome and outputs a list of all possible locations within any given edit distance…

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exceRpt
Web

exceRpt

Allows users to processing of RNA-Seq data. exceRpt is a pipeline for RNA-Seq…

Allows users to processing of RNA-Seq data. exceRpt is a pipeline for RNA-Seq library preparation. The software processes each sample independently through a cascade of read-alignment steps designed…

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ISEA
Desktop

ISEA Iterative Seed-Extension Algorithm

Provides an iterative seed-extension algorithm for de novo assembly. ISEA…

Provides an iterative seed-extension algorithm for de novo assembly. ISEA comports five steps: (i) preprocessing, (ii) graph and seed building, (iii) contig extension, (iv) merging and (v)…

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RNA workbench
Server

RNA workbench

Establishes a central, redistributable workbench for scientists and programmers…

Establishes a central, redistributable workbench for scientists and programmers working with RNA-related data. The RNA workbench builds a sustainable community around it. This platform is unique in…

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GateKeeper
Desktop

GateKeeper

Reduces the need of alignment verification in DNA read mapping. GateKeeper is a…

Reduces the need of alignment verification in DNA read mapping. GateKeeper is a hardware acceleration system for alignment filtering designed to utilize the large amounts of parallelism offered by…

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LEAP
Desktop

LEAP

Provides a bit vectorized de Bruijn sequence based optimization. LEAP is a…

Provides a bit vectorized de Bruijn sequence based optimization. LEAP is a general dynamic-programming solution for the Leaping Toad problem based on the Landau-Vishkin algorithm. This package…

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Scallop
Desktop

Scallop

Enables accurate identification of multi-exon transcripts and lowly expressed…

Enables accurate identification of multi-exon transcripts and lowly expressed transcripts. Scallop is an accurate reference-based transcript assembler. The software uses a novel algorithm to…

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Ngmlr
Desktop

Ngmlr coNvex Gap-cost alignMent for Long Reads

Aligns PacBio or Oxford Nanopore to (large) reference genomes. NGMLR is an…

Aligns PacBio or Oxford Nanopore to (large) reference genomes. NGMLR is an aligner for long reads based on a previous seed-and-extend short read aligner NGM28, extended with a new segmented convex…

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Qtip
Desktop

Qtip

Operates alongside and in cooperation with an aligner like Bowtie 2. Qtip runs…

Operates alongside and in cooperation with an aligner like Bowtie 2. Qtip runs alongside a read aligner and builds an input model, simulates tandem reads, aligns those using the same aligner and…

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MashMap
Desktop

MashMap

Maps a read against a reference region if and only if its estimated alignment…

Maps a read against a reference region if and only if its estimated alignment identity is above a specified threshold. MashMap is a fast approximate algorithm for mapping long reads that scales to…

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viGEN
Desktop

viGEN

Combines existing well-known and novel RNA-seq tools for not only detection and…

Combines existing well-known and novel RNA-seq tools for not only detection and quantification of viral RNA, but also variants in the viral transcripts. ViGEN includes 4 major modules: the first…

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SNP-o-matic
Desktop

SNP-o-matic

Maps short sequence reads to a reference genome with a list of putative…

Maps short sequence reads to a reference genome with a list of putative variable positions. SNP-o-matic allows rapid processing of large volumes of sequencing data. It first indexes the reference…

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BigBWA
Desktop

BigBWA

Uses the Big Data technology Hadoop to boost the performance of the…

Uses the Big Data technology Hadoop to boost the performance of the Burrows-Wheeler Aligner (BWA). Important reductions in the execution times were observed when using this tool. In addition, BigBWA…

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BatMis
Desktop

BatMis Basic Alignment tool for Mismatches

An efficient method to align short reads to a reference allowing k mismatches.…

An efficient method to align short reads to a reference allowing k mismatches. BatMis is a Burrows-Wheeler transformation based aligner that uses a seed and extend approach, and it is an exact…

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Automation
Desktop

Automation

An automated method for aligning nanopore data to a reference through the use…

An automated method for aligning nanopore data to a reference through the use of hidden Markov models. Several features that arise from prior processing steps and from the class of enzyme used can be…

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RNA-Rocket
Web

RNA-Rocket

A free service that provides access to RNA-Seq and ChIP-Seq analysis tools for…

A free service that provides access to RNA-Seq and ChIP-Seq analysis tools for studying infectious diseases. The site makes available thousands of pre-indexed genomes, their annotations, and the…

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PSGInfer
Desktop

PSGInfer

Inference of alternative splicing from RNA-Seq data with probabilistic splice…

Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs.

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Fast…
Desktop

Fast Seed-and-Vote Aligner

Extracts seeds from the read to vote the coordinate. FSVA is based on the…

Extracts seeds from the read to vote the coordinate. FSVA is based on the seed-and-vote strategy to build a hash table for a reference genome. It lies in the longer seed in order to permit improved…

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ANGSD
Desktop

ANGSD

Analyses next generation sequencing (NGS) data. ANGSD can handle a number of…

Analyses next generation sequencing (NGS) data. ANGSD can handle a number of different input types from mapped reads to imputed genotype probabilities. Most methods take genotype uncertainty into…

CAP3
Web

CAP3

The third generation of the CAP sequence assembly program. The CAP3 program…

The third generation of the CAP sequence assembly program. The CAP3 program includes a number of improvements and new features. The program has a capability to clip 58 and 38 low-quality regions of…

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G-SNPM
Desktop

G-SNPM GPU-SNP Mapping

Maps a sequence representative of a single nucleotide polymorphism (SNP)…

Maps a sequence representative of a single nucleotide polymorphism (SNP) against a reference sequence to determine its absolute position in that sequence. G-SNPM intends to remap the SNPs chromosomal…

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CloudAligner
Desktop

CloudAligner

Achieves higher performance, covers most primary features, is more accurate,…

Achieves higher performance, covers most primary features, is more accurate, and has a user-friendly interface. CloudAligner was also designed to be able to deal with long sequences. The performance…

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Yara
Desktop

Yara Yet another read aligner

An exact tool for aligning DNA sequencing reads to reference genomes. Main…

An exact tool for aligning DNA sequencing reads to reference genomes. Main features: exhaustive enumeration of sub-optimal end-to-end alignments under the edit distance; alignment of single-end,…

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CGAP-Align
Desktop

CGAP-Align

Achieves a performance improvement over BWA without sacrificing recall or…

Achieves a performance improvement over BWA without sacrificing recall or precision. This is accomplished through the use of Suffix Tarray, a novel data structure combining elements of Suffix Array…

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TAPyR
Desktop

TAPyR

An efficient Tool for the local Alignment of Pyrosequencing Reads produced by…

An efficient Tool for the local Alignment of Pyrosequencing Reads produced by the GS FLX (454) Genome Analyzer technology against a reference genome sequence.

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NanoBLASTer
Desktop

NanoBLASTer

Aligns long nanopore reads. NanoBLASTer includes several novel enhancements to…

Aligns long nanopore reads. NanoBLASTer includes several novel enhancements to maintain high sensitivity and high performance in the presence of high error rates that would otherwise limit the…

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MECAT
Desktop

MECAT Mapping Error Correction and de novo Assembly Tool

Employs novel alignment and error correction algorithms that are much more…

Employs novel alignment and error correction algorithms that are much more efficient than the state of art of aligners and error correction tools. MECAT can be used for effectively de novo assembling…

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BALAUR
Desktop

BALAUR

A privacy preserving read mapping technique for hybrid clouds that securely…

A privacy preserving read mapping technique for hybrid clouds that securely outsources a significant portion of the read-mapping task to the public cloud, while being highly competitive with existing…

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Benchmark
Dataset

Benchmark

A comparison of different NGS read mappers. Detailed performance comparisons of…

A comparison of different NGS read mappers. Detailed performance comparisons of NGS read aligners are provided. Benchmarks only measure specific aspects and may not be used to claim any universal…

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BBT
Desktop

BBT BioBloom tools

A Bloom filter-based sequence-screening tool that is faster than BWA, Bowtie 2…

A Bloom filter-based sequence-screening tool that is faster than BWA, Bowtie 2 (popular alignment algorithms) and FACS (a membership query algorithm). BioBloom Tools delivers accuracies comparable…

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BIMA
Desktop

BIMA

A next generation sequencing (NGS) mapping and alignment algorithm customized…

A next generation sequencing (NGS) mapping and alignment algorithm customized to process mate pair library sequencing. Mate Pair sequencing is a comprehensive and cost effective method for detecting…

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SPARTA
Desktop

SPARTA

A reference-based bacterial RNA-seq analysis workflow application for…

A reference-based bacterial RNA-seq analysis workflow application for single-end Illumina reads. SPARTA is turnkey software that simplifies the process of analyzing RNA-seq data sets, making…

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BitMapper
Desktop

BitMapper

An efficient reads mappers for short reads of equal length. It is designed to…

An efficient reads mappers for short reads of equal length. It is designed to output all mapping locations for each reads. BitMapper is useful for applications, such as ChIP-seq experiments, CNVs…

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MICA-aligner
Desktop

MICA-aligner

A short-read aligner designed to fully utilize the computing power of many…

A short-read aligner designed to fully utilize the computing power of many integrated core (MIC). MICA-aligner accepts input reads in FASTA/FASTQ format and outputs alignment results in SAM/BAM…

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ALFALFA
Desktop

ALFALFA A Long Fragment Aligner/A Long Fragment Aligner

Achieves high performance in accurately mapping long (>500bp) single-end and…

Achieves high performance in accurately mapping long (>500bp) single-end and paired-end reads to gigabase-scale reference genomes, while remaining competitive for mapping shorter (>100bp)…

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GBSA
Desktop

GBSA GNU Backward Search Aligner

An inexact mapping algorithm compatible with any backward search approach.…

An inexact mapping algorithm compatible with any backward search approach. Although not intended as a complete sequence mapping tool, the proposed algorithm could be used as a preprocessing step to…

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BLASR
Desktop

BLASR Basic Local Alignment with Successive Refinement

A method for mapping Single Molecule Sequencing (SMS) reads that are thousands…

A method for mapping Single Molecule Sequencing (SMS) reads that are thousands of bases long, with divergence between the read and genome dominated by insertion and deletion error. The method is…

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Hobbes
Desktop

Hobbes

A software package designed for fast and accurate alignment of NGS reads and…

A software package designed for fast and accurate alignment of NGS reads and specialized in identifying all mapping locations of each read.

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benchNGS
Dataset

benchNGS

A benchmark to assess biological relevance of programs for reference genome…

A benchmark to assess biological relevance of programs for reference genome alignments has been developed and applied to compare the most popular freely available programs. All programs show similar…

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MaxSSmap
Desktop

MaxSSmap

Background Programs based on hash tables and Burrows-Wheeler are very fast for…

Background Programs based on hash tables and Burrows-Wheeler are very fast for mapping short reads to genomes but have low accuracy in the presence of mismatches and gaps. Such reads can be aligned…

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FANSe
Desktop

FANSe

A mapping algorithm which can map a billion reads in hours with ultimate and…

A mapping algorithm which can map a billion reads in hours with ultimate and robust accuracy.

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NovoAlignCS
Desktop

NovoAlignCS

Enables the use of multiple servers in a cluster to align a file of reads.…

Enables the use of multiple servers in a cluster to align a file of reads. NovoalignCS is the NovoCraft’s aligner for ABI SOLiD colour space reads, operation is similar to standard Novoalign with…

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G-CNV
Desktop

G-CNV GPU-copy number variation

A graphics processing unit (GPU)-based tool for preparing data to detect copy…

A graphics processing unit (GPU)-based tool for preparing data to detect copy number variations (CNVs) with read-depth methods. G-CNV can be used to (i) filter low-quality sequences, (ii) mask…

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CLC Genomics…
Desktop

CLC Genomics Workbench

Allows to analyze, compare, and visualize next generation sequencing (NGS)…

Allows to analyze, compare, and visualize next generation sequencing (NGS) data. CLC Genomics Workbench offers a complete and customizable solution for genomics, transcriptomics, epigenomics, and…

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TreQ
Desktop

TreQ

A read mapper for high-throughput DNA sequencing reads, in particular one to…

A read mapper for high-throughput DNA sequencing reads, in particular one to several hundred nucleotides in length, and for large edit distance between sequencing read and match in the reference…

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SToRM
Desktop

SToRM

A software tool primarily proposed for mapping SOLiD reads or Illumina reads to…

A software tool primarily proposed for mapping SOLiD reads or Illumina reads to a reference genome.

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MOM
Desktop

MOM Maximum Oligonucleotide Mapping

Is based on the concept of query matching that is designed to capture a maximal…

Is based on the concept of query matching that is designed to capture a maximal length match within the short read satisfying the user defined error parameters. The MOM query matching approach thus…