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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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AlignerBoost
Desktop

AlignerBoost

Estimates mapping quality of ambiguously mapped next generation sequencing…

Estimates mapping quality of ambiguously mapped next generation sequencing (NGS) reads. AlignerBoost utilizes a Bayesian-based framework, and tests with both simulated and real DNA-seq and RNA-seq…

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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.…

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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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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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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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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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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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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

An ultrafast, memory-efficient and highly accurate pair-end read merger.

An ultrafast, memory-efficient and highly accurate pair-end read merger.

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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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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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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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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…

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RMAP
Desktop

RMAP

It is aimed to map accurately reads from the next-generation sequencing…

It is aimed to map accurately reads from the next-generation sequencing technology.

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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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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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Teaser
Desktop
Web

Teaser

An analytical framework for benchmarking NGS read mappers. Teaser allows…

An analytical framework for benchmarking NGS read mappers. Teaser allows researchers to identify the optimal mapper, parameter set and mapping quality thresholds for data sets that mimic their real…

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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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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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ARDEN
Desktop

ARDEN Artificial Reference Driven Estimation of false positives in NGS data

A benchmark that estimates error rates based on real experimental reads and an…

A benchmark that estimates error rates based on real experimental reads and an additionally generated artificial reference genome. ARDEN allows the computation of error rates specifically for a…

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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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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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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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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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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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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 that are specified at the outset. SNP-o-matic allows the rapid processing of large volumes of sequencing…

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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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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…

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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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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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Arioc
Desktop

Arioc

A read aligner that uses GPU-based parallel sort and reduction techniques to…

A read aligner that uses GPU-based parallel sort and reduction techniques to identify high-priority locations where potential alignments may be found. The Arioc pipeline implementation consists of…

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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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SOAPaligner
Desktop

SOAPaligner Short Oligonucleotide Analysis Package

Enables ultrafast and memory-efficient alignment of massive short sequencing…

Enables ultrafast and memory-efficient alignment of massive short sequencing reads. SOAPaligner permits users to index the reference and perform reads alignment. It can tolerate as low as 60 per cent…

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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…

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YOABS
Algorithm

YOABS Yet Other Aligner of Biological Sequences

Combines the advantages of both hash- and trie-based algorithms. YOABS is a…

Combines the advantages of both hash- and trie-based algorithms. YOABS is a long alignment algorithm that does not use the seed-and-extend paradigm and, hence, does not bear those computational…

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SeqAlto
Desktop

SeqAlto

An aligner specifically designed for Illumina reads of length greater or equal…

An aligner specifically designed for Illumina reads of length greater or equal to about 100-bp. It takes advantage of this longer read length to provide fast alignment rates and accurate placement of…

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YAHA
Desktop

YAHA

A flexible, sensitive and accurate hash-based DNA aligner for relatively long…

A flexible, sensitive and accurate hash-based DNA aligner for relatively long queries that operates in three distinct modes. YAHA uses a directed acyclic graph to find the optimal set of alignments…

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PEANUT
Desktop

PEANUT ParallEl AligNment UTility

A highly parallel GPU-based read mapper. By exploiting the massive parallelism…

A highly parallel GPU-based read mapper. By exploiting the massive parallelism of modern graphics processors and a novel index data structure (the q-group index), PEANUT achieves supreme speed…

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CUSHAW2-GPU
Desktop

CUSHAW2-GPU Parallel Gapped Read Alignment

This program (based on CUSHAW2) is designed and optimized for Kepler-based…

This program (based on CUSHAW2) is designed and optimized for Kepler-based GPUs, but still workable on earlier-generation Fermi-based ones.

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Rabema
Desktop

Rabema Read Alignment BEnchMArk

Provides a benchmark method for read mappers. Rabema consists of a strict…

Provides a benchmark method for read mappers. Rabema consists of a strict definition of the read mapping problem and of tools to evaluate the result of arbitrary read mappers supporting the SAM…

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CircularMapper
Desktop

CircularMapper

Permits users to perfect mappings on circular genomes. CircularMapper uses BWA…

Permits users to perfect mappings on circular genomes. CircularMapper uses BWA to create maps.

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ESTmapper
Desktop

ESTmapper

Allows users to align DNA sequences to genomes and uses such alignments to…

Allows users to align DNA sequences to genomes and uses such alignments to cluster expressed sequence tags (ESTs). ESTmapper algorithm consists of the following steps: it (i) preprocesses the genome,…

Vmatch
Desktop

Vmatch

Solves efficiently large scale sequence matching tasks. Vmatch is a versatile…

Solves efficiently large scale sequence matching tasks. Vmatch is a versatile software that can process sequences over any user defined alphabet not larger than 250 symbols. This method fully…

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Igrep
Web

Igrep

Provides a CUDA implementation of agrep algorithm for approximate nucleotide…

Provides a CUDA implementation of agrep algorithm for approximate nucleotide sequence matching. Igrep is a program that requires no indexing at all, yet resulting in remarkably reduced execution time.

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Dascrubber
Desktop

Dascrubber DAzzler Read SCRUBBing Suite

Provides a pipeline that one can use to scrub reads and if desired to scrub the…

Provides a pipeline that one can use to scrub reads and if desired to scrub the alignment piles. Dascrubber is a complete end-to-end scrubber for removing all artifacts and low quality segments from…

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Nanonet
Desktop

Nanonet

Performs event detection step and segmentation for both 1D and 2D base-calling…

Performs event detection step and segmentation for both 1D and 2D base-calling that runs locally using multiple Central Processing Units (CPUs). Nanonet provides also an interface for training…

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COSINE
Desktop

COSINE

Aligns long sequences with high variations or errors including insertions and…

Aligns long sequences with high variations or errors including insertions and deletions to the target. COSINE has a predictable computational resource usage for mapping reads from E. coli genome, S.…

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pbdagcon
Desktop

pbdagcon

Encodes multiple sequence alignment. pbdagcon implements Directed Acyclic Graph…

Encodes multiple sequence alignment. pbdagcon implements Directed Acyclic Graph Consensus (DAGCon), a sequence consensus algorithm that uses Directed Acyclic Graphs (DAG). The software aligns…

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pbalign
Desktop

pbalign

Aligns PacBio reads to reference sequences. pbalign is a part of the PacBio…

Aligns PacBio reads to reference sequences. pbalign is a part of the PacBio Bioinformatics tools. The software filters aligned reads in accordance with user-specific filtering criteria, and then…

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BBMap
Desktop

BBMap

Uses as a splice-aware aligner for short and long reads. BBMap is shown to be a…

Uses as a splice-aware aligner for short and long reads. BBMap is shown to be a fast and accurate aligner, capable of correctly handling an overall wider variety of references, reads, and mutations…

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NovoAlign
Desktop

NovoAlign

Uses for mapping of short reads onto a reference genome from Illumina, Ion…

Uses for mapping of short reads onto a reference genome from Illumina, Ion Torrent, and 454 NGS platforms. NovoAlign is packed with unsurpassed features like alignment quality scores using posterior…

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DIDA
Desktop

DIDA

A framework that performs the large-scale alignment tasks by distributing the…

A framework that performs the large-scale alignment tasks by distributing the indexing and alignment stages into smaller subtasks over a cluster of compute nodes. First, the targets are partitioned…

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Genomatix…
Desktop

Genomatix Solutions

With their unique combination of proprietary algorithms and comprehensive data…

With their unique combination of proprietary algorithms and comprehensive data background, all our solutions do more than enable you to efficiently and effectively analyze and interpret biological…

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NextGENe
Desktop

NextGENe

Software for Next Generation (NGS) Sequence Analysis.

Software for Next Generation (NGS) Sequence Analysis.

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TMAP
Desktop

TMAP Torrent Mapping Alignment Program

Alignment software for short and long nucleotide sequences produced by…

Alignment software for short and long nucleotide sequences produced by next-generation sequencing technologies.

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VelociMapper
Desktop

VelociMapper

Our new accelerated alignment tool for mapping data from next-generation DNA…

Our new accelerated alignment tool for mapping data from next-generation DNA sequencing systems.

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WHAM
Desktop

WHAM Wisconsin’s High-throughput Alignment Method

A high-throughput sequence alignment tool developed at University of…

A high-throughput sequence alignment tool developed at University of Wisconsin-Madison.