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Genome assembly software tools | De novo sequencing data analysis

High-throughput sequencing produces large amounts of long or short DNA reads which require assembly process to generate the complete genome sequence. De novo genome assembler programs have been written to detect overlaps between reads, to assemble…
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Trinity
Desktop

Trinity

A method for the efficient and robust de novo reconstruction of transcriptomes…

A method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.

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Ray
Desktop

Ray

Assembles reads obtained with new sequencing technologies (Illumina, 454,…

Assembles reads obtained with new sequencing technologies (Illumina, 454, SOLiD) using MPI 2.2. Ray allows to reduce the number of contigs and the number of errors. It can serve as a basis to develop…

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SSAKE
Desktop

SSAKE

Provides a de novo assembler for short DNA sequence reads. SSAKE is designed to…

Provides a de novo assembler for short DNA sequence reads. SSAKE is designed to help leverage the information from short sequences reads by assembling them into contigs and scaffolds that can be used…

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Orione
Web

Orione

A Galaxy-based framework consisting of publicly available research software and…

A Galaxy-based framework consisting of publicly available research software and specifically designed pipelines to build complex, reproducible workflows for next-generation sequencing microbiology…

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MHAP
Desktop

MHAP MinHash Alignment Process

A reference implementation of a probabilistic sequence overlapping algorithm.…

A reference implementation of a probabilistic sequence overlapping algorithm. MHAP is designed to efficiently detect all overlaps between noisy long-read sequence data. It efficiently estimates…

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LQS
Desktop

LQS

Computes an improved consensus sequence for the assembly. LQS uses accurate…

Computes an improved consensus sequence for the assembly. LQS uses accurate short-read data and/or Pacific Biosciences circular consensus reads to correct error-prone long reads sufficiently for…

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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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PBcR
Desktop

PBcR PacBio Corrected Reads

An approach that utilizes short, high-identity sequences to correct the error…

An approach that utilizes short, high-identity sequences to correct the error inherent in long, single-molecule sequences. PBcR, implemented as part of the Celera Assembler, trims and corrects…

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SGA
Desktop

SGA String Graph Assembler

Assembles large genomes from high coverage short read data. SGA is designed as…

Assembles large genomes from high coverage short read data. SGA is designed as a modular set of programs, which are used to form an assembly pipeline. SGA implements a set of assembly algorithms…

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ABySS
Desktop

ABySS

Assembles the very large data sets produced by sequencing individual human…

Assembles the very large data sets produced by sequencing individual human genomes. ABySS is a parallelized sequence assembler. The primary innovation in ABySS is a distributed representation of a de…

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FALCON
Desktop

FALCON

Allows alignment of long reads for consensus and assembly. FALCON is a set of…

Allows alignment of long reads for consensus and assembly. FALCON is a set of tools based on a hierarchical genome assembly process. The software follows a "Hierarchical Genome Assembly…

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MIRA
Desktop

MIRA Mimicking Intelligent Read Assembly

Uses a Swiss army knife of sequence assembly developed and used in the past 16…

Uses a Swiss army knife of sequence assembly developed and used in the past 16 years to get assembly jobs done efficiently - and especially accurately. MIRA is a whole genome shotgun (WGS) and EST…

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DISCOVAR de…
Desktop

DISCOVAR de novo

A large (and small) de novo genome assembler. DISCOVAR de novo quickly…

A large (and small) de novo genome assembler. DISCOVAR de novo quickly generates highly accurate and complete assemblies using the same single library data. It requires reads from only a single…

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DISCOVAR
Desktop

DISCOVAR

A variant caller and small genome assembler. The heart of DISCOVAR is a de novo…

A variant caller and small genome assembler. The heart of DISCOVAR is a de novo genome assembler, one that is accurate enough to produce assemblies that can be used for variant calling given a…

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SHARCGS
Desktop

SHARCGS

Assembles short-read (25–40-mer) data with high accuracy and speed. SHARCGS…

Assembles short-read (25–40-mer) data with high accuracy and speed. SHARCGS allows to exploit novel sequencing technologies by assembling sequence contigs de novo with high confidence and by…

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Supernova
Desktop

Supernova

Allows to create true diploid de novo assemblies. Supernova can separate…

Allows to create true diploid de novo assemblies. Supernova can separate homologous chromosomes over long distances, in this sense capturing the true biology of a diploid genome. The Supernova…

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Platanus
Desktop

Platanus

A de novo sequence assembler that can reconstruct genomic sequences of highly…

A de novo sequence assembler that can reconstruct genomic sequences of highly heterozygous diploids from massively parallel shotgun sequencing data.

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SOAPdenovo
Desktop

SOAPdenovo

Provides a short-read assembly method that can build a de novo draft assembly…

Provides a short-read assembly method that can build a de novo draft assembly for the human-sized genomes. SOAPdenovo is specially designed to assemble Illumina GA short reads. It creates new…

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HGAP
Desktop

HGAP Hierarchical Genome-Assembly Process

A program for high-quality de novo microbial genome assemblies using only a…

A program for high-quality de novo microbial genome assemblies using only a single, long-insert shotgun DNA library in conjunction with Single Molecule, Real-Time (SMRT) DNA sequencing. The process…

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A5
Desktop

A5

Produces assemblies of quality comparable to a leading assembly algorithm,…

Produces assemblies of quality comparable to a leading assembly algorithm, SOAPdenovo, without any prior knowledge of the particular genome being assembled. A5 is an assembly pipeline that simplifies…

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VirusTAP
Web

VirusTAP Virus genome-Targeted Assembly Pipeline

Assembles virus genomes from next generation sequencing (NGS) reads. VirusTAP…

Assembles virus genomes from next generation sequencing (NGS) reads. VirusTAP is a web based platforms for the viral genome that performs the following informatics steps: (i) quality trimming and…

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ALLPATHS-LG
Desktop

ALLPATHS-LG

Provides a whole‐genome shotgun assembler that can generate high‐quality…

Provides a whole‐genome shotgun assembler that can generate high‐quality genome assemblies using short reads (~100bp) such as those produced by the new generation of sequencers. The ALLPATHS-LG…

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Redundans
Desktop

Redundans

A pipeline that specifically deals with the assembly of heterozygous genomes by…

A pipeline that specifically deals with the assembly of heterozygous genomes by introducing a step to recognise and selectively remove alternative heterozygous contigs. Redundans consists of three…

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Velvet
Desktop

Velvet

Manipulates de Bruijn graphs (DBG) for genomic sequence assembly. Velvet is a…

Manipulates de Bruijn graphs (DBG) for genomic sequence assembly. Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454. It takes in…

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Racon
Algorithm

Racon Rapid Consensus

Generates high quality consensus sequences with a single instruction multiple…

Generates high quality consensus sequences with a single instruction multiple data (SIMD) accelerated. Racon is based on tests with PacBio and Oxford Nanopore datasets. It enables consensus genomes…

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m6aViewer
Desktop

m6aViewer

Analyzes and visualizes N6-methyl-adenosine (m6A) peaks from sequencing data.…

Analyzes and visualizes N6-methyl-adenosine (m6A) peaks from sequencing data. m6aViewer is a cross-platform application that implements an m6A peak-calling algorithm. It assists in detection of…

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Minimap/miniasm
Desktop

Minimap/miniasm

A mapper, minimap, and a de novo assembler, miniasm, for efficiently mapping…

A mapper, minimap, and a de novo assembler, miniasm, for efficiently mapping and assembling single molecule real-time (SMRT) and Oxford Nanopore technologies (ONT) reads without an error correction…

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MaSuRCA
Desktop

MaSuRCA

Allows variable read lengths while tolerating a significant level of sequencing…

Allows variable read lengths while tolerating a significant level of sequencing error. MaSuRCa combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. It…

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PE-Assembler
Desktop

PE-Assembler

Allows to handle large datasets and produce highly contiguous and accurate…

Allows to handle large datasets and produce highly contiguous and accurate assemblies within reasonable time. PE-Assembler is based on simple 3 extension approach and does not involve representing…

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SIMBA
Desktop

SIMBA SImple Manager for Bacterial Assemblies

Manages assembly projects of bacterial genomes with Next Generation Sequencing…

Manages assembly projects of bacterial genomes with Next Generation Sequencing (NGS) platforms. SIMBA is composed of three parts: (i) projects is a module which permits to administer sequencing…

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Edena
Desktop

Edena

Exploits the pairing information issued from inserts of potentially any length.…

Exploits the pairing information issued from inserts of potentially any length. Edena determines suited overlaps cutoffs according to the contextual coverage, reducing thus the need for manual…

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PRICE
Desktop

PRICE Paired-Read Iterative Contig Extension

A software for the targeted de novo assembly of genomic sequence from…

A software for the targeted de novo assembly of genomic sequence from large-scale genomic or metagenomic datasets. PRICE is designed with paired-end data in mind but does not require such data. The…

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SparseAssembler
Desktop

SparseAssembler

Contains sparse graph approach to de novo genome assembly. SparseAssembler…

Contains sparse graph approach to de novo genome assembly. SparseAssembler consistently produces comparable results to the current state-of-the-art de Bruijn graph-based assemblers. It demands…

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Minimus
Desktop

Minimus

Assemblies small data-sets. Minimus uses the Smith-Waterman hash-overlap…

Assemblies small data-sets. Minimus uses the Smith-Waterman hash-overlap program for extracting individual genes from shotgun datasets and allows users to analyze newly sequenced organisms. The…

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Assemblathon
Desktop

Assemblathon

Aims to comprehensively assess the state of the art in de novo assembly methods…

Aims to comprehensively assess the state of the art in de novo assembly methods when applied to current sequencing technologies. Assemblathon is a set of periodic collaborative efforts that all help…

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NOVOPlasty
Desktop

NOVOPlasty

An algorithm specifically developed for the de novo assembly of mitochondrial…

An algorithm specifically developed for the de novo assembly of mitochondrial and chloroplast genomes from whole genome data. NOVOPlasty starts with storing the sequences into a hash table, which…

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Minia
Desktop

Minia

Assembles a human genome on a desktop computer in a day. Minia is based on a de…

Assembles a human genome on a desktop computer in a day. Minia is based on a de Bruijn graph. It combines the Bloom filter, the critical false positives structure and the marking structure. The tool…

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KBase
Dataset

KBase KBase

Supplies an unified environment for predictive biology which gathers data…

Supplies an unified environment for predictive biology which gathers data tools, and their associated interfaces. KBase aims to ease creation, execution and collaboration around reproducible analyses…

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BugBuilder
Desktop

BugBuilder

Can carry out assembly and analysis of microbial genome sequences. BugBuilder…

Can carry out assembly and analysis of microbial genome sequences. BugBuilder takes sequence reads as inputs and produces submission-ready annotated genome assemblies, with ease-of-use prioritised to…

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Canu
Desktop

Canu

Is specifically designed for noisy single-molecule sequences. Canu introduces…

Is specifically designed for noisy single-molecule sequences. Canu introduces support for nanopore sequencing, halves depth-of-coverage requirements, and improves assembly continuity while…

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PASHA
Desktop

PASHA

Takes advantage of hybrid computing architectures consisting of both…

Takes advantage of hybrid computing architectures consisting of both shared-memory multi-core CPUs and distributed-memory compute clusters to gain efficiency and scalability. PASHA is a parallelized…

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deBGR
Desktop

deBGR

Supplies an approximate representation of the weighted de Bruijn Graph. deBGR…

Supplies an approximate representation of the weighted de Bruijn Graph. deBGR was built on the prototype k-mer counter Squeakr.

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spectrassembler
Desktop

spectrassembler

Computes the layout of raw nanopore reads. spectrassembler computes an assembly…

Computes the layout of raw nanopore reads. spectrassembler computes an assembly from the all-vs-all raw read mapping. It achieves improved quality through a coverage-based consensus generation…

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Kollector
Desktop

Kollector

Uses thousands of transcript sequences concurrently to inform the localized…

Uses thousands of transcript sequences concurrently to inform the localized assembly of corresponding gene loci. Kollector reconstructs introns and novel sequences within these loci, and scales well…

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LOCAS
Desktop

LOCAS

Assembles short reads of next generation sequencing (NGS) technologies at low…

Assembles short reads of next generation sequencing (NGS) technologies at low coverage. LOCAS uses a mismatch sensitive overlap-layout-consensus approach. It assembles homologous regions in a…

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VICUNA
Desktop

VICUNA

A de novo assembly program targeting populations with high mutation rates.

A de novo assembly program targeting populations with high mutation rates.

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CloudBrush
Desktop

CloudBrush

Detects structural defects by examining the neighboring reads of a specific…

Detects structural defects by examining the neighboring reads of a specific read for sequencing errors and adjusting the edges of the string graph. CloudBrush is a conservative assembler that…

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Organelle_PBA
Desktop

Organelle_PBA

Assemblies chloroplast and mitochondrial genomes. Organelle_PBA selects the…

Assemblies chloroplast and mitochondrial genomes. Organelle_PBA selects the chloroplast reads from a whole genome sequencing (WGS) pool, maps the reads to a reference sequence from a closely related…

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iAssembler
Desktop

iAssembler

Assembles large-scale expressed sequence tags (EST) datasets and automatically…

Assembles large-scale expressed sequence tags (EST) datasets and automatically identifies and correct assembly errors. iAssembler employs an iterative assembly strategy and automated assembly error…

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Taipan
Desktop

Taipan

Implements a read fragment assembly algorithm for de-novo genome of short reads…

Implements a read fragment assembly algorithm for de-novo genome of short reads generated by sequencing machines. Taipan uses a combination of the greedy extension and the overlap graph method. A…

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MITObim
Desktop

MITObim MITOchondrial Baiting and Iterative Mapping

An in silico approach for the reconstruction of complete mitochondrial genomes…

An in silico approach for the reconstruction of complete mitochondrial genomes of non-model organisms directly from next-generation sequencing (NGS) data-mitochondrial baiting and iterative mapping.…

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SATRAP
Desktop

SATRAP SOLiD Assembler TRAnslation Program

A computer program designed to efficiently translate de novo assembled…

A computer program designed to efficiently translate de novo assembled color-space sequences into a base-space format. The program was tested and validated using simulated and real transcriptomic…

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SNPsplit
Desktop

SNPsplit

An allele-specific alignment sorter designed to read files in SAM/BAM format…

An allele-specific alignment sorter designed to read files in SAM/BAM format and determine the allelic origin of reads or read-pairs that cover known single nucleotide polymorphic (SNP) positions.…

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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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LightAssembler
Desktop

LightAssembler

A lightweight assembly algorithm designed to be executed on a desktop machine.…

A lightweight assembly algorithm designed to be executed on a desktop machine. It uses a pair of cache oblivious Bloom filters, one holding a uniform sample of g-spaced sequenced k-mers and the other…

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BCALM
Desktop

BCALM

An open-source parallel and low-memory tool for the compaction of de Bruijn…

An open-source parallel and low-memory tool for the compaction of de Bruijn graphs. BCALM 2 constructed the compacted de Bruijn graph of a human genome sequencing dataset in 76 mins and 3 GB of…

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KREATION
Desktop

KREATION Kmer Range EstimATION

An automatic method for limiting the number of kmer values without a…

An automatic method for limiting the number of kmer values without a significant loss in assembly quality but with savings in assembly time. This is a step forward to making multi-kmer methods more…

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StriDe
Desktop

StriDe

An assembler that has advantages of both string and de Bruijn graphs. First,…

An assembler that has advantages of both string and de Bruijn graphs. First, the reads are decomposed adaptively only in error-prone regions. Second, each paired-end read is extended into a long read…

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hybridSPAdes
Desktop

hybridSPAdes

An algorithm for assembling short and long reads. hybridSPAdes generates…

An algorithm for assembling short and long reads. hybridSPAdes generates accurate assemblies (even in projects with relatively low coverage by long reads) thus reducing the overall cost of genome…

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EPGA
Desktop

EPGA

An algorithm which extracts paths from De Bruijn graph for genome assembly.…

An algorithm which extracts paths from De Bruijn graph for genome assembly. EPGA uses a score function to evaluate extension candidates based on the distributions of reads and insert size. The…

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JR-Assembler
Desktop

JR-Assembler

Assembles de novo short read sequencing data. An assembler for the de novo…

Assembles de novo short read sequencing data. An assembler for the de novo assembly of large genomes using short sequence reads via jumping extension and read remapping. JR-Assembler extends a read…

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VirAmp
Web

VirAmp

A web-based semi-de novo fast virus genome assembly pipeline designed for…

A web-based semi-de novo fast virus genome assembly pipeline designed for extremely high coverage NGS data. VirAmp is a collection of existing tools, combined into a single Galaxy interface. Users…

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Meraculous
Desktop

Meraculous

Implements an algorithm for whole genome assembly of deep paired-end short…

Implements an algorithm for whole genome assembly of deep paired-end short reads. Meraculous relies on an efficient and conservative traversal of a subgraph of the k-mer de Bruijn graph (DBG) of…

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QSRA
Desktop

QSRA Quality-value guided Short Read Assembler

Takes advantage of quality-value scores as a further method of dealing with…

Takes advantage of quality-value scores as a further method of dealing with error. QSRA provides a step closer to the goal of de novo assembly of complex genomes, improving upon the original VCAKE…

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GenSeed-HMM
Desktop

GenSeed-HMM

Provides a method to run progressive sequence assembly pipelines that are…

Provides a method to run progressive sequence assembly pipelines that are directly targeted at sequences of interest. GenSeed-HMM is a completely revised and highly incremented version of GenSeed.…

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Telescoper
Desktop

Telescoper

Extends long paths through a series of read-overlap graphs and evaluates them…

Extends long paths through a series of read-overlap graphs and evaluates them based. Telescoper uses short- and long-insert libraries in an integrated way throughout the assembly process. It produces…

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BASE
Desktop

BASE

A de novo genome assembler using next generation sequencing (NGS) data. BASE…

A de novo genome assembler using next generation sequencing (NGS) data. BASE enhances the classic seed-extension approach by indexing the reads efficiently to generate adaptive seeds that have high…

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HGA
Desktop

HGA Hierarchical Genome Assembly

A methodology designed to take advantage of a high coverage by independently…

A methodology designed to take advantage of a high coverage by independently assembling disjoint subsets of reads, combining the assemblies of the subsets, and finally re-assembling the combined…

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Rascaf
Desktop

Rascaf RnA-SCAFfolder

A tool leveraging long-range continuity information from intron spanning RNA…

A tool leveraging long-range continuity information from intron spanning RNA sequencing read pairs to detect new contig connections. Rascaf is a tool used to the alignments of RNA-seq reads to…

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VAGUE
Desktop

VAGUE Velvet Assembler Graphical User Environment

A multi-platform graphical front-end for Velvet. VAGUE aims to make sequence…

A multi-platform graphical front-end for Velvet. VAGUE aims to make sequence assembly accessible to a wider audience and to facilitate better usage amongst existing users of Velvet.

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PERGA
Desktop

PERGA Paired-End Reads Guided Assembler

A de novo paired-end reads assembler. PERGA can generate large and accurate…

A de novo paired-end reads assembler. PERGA can generate large and accurate assemblies using the greedy-like prediction strategy to handle branches and errors to give much better extensions. By using…

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MELC Genomics
Desktop

MELC Genomics

Performs a genome assembly. MELC Genomics is a platform with independent…

Performs a genome assembly. MELC Genomics is a platform with independent modules which have to be executed through a web browser interface. The software allows users to run different tasks such as…

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VGW
Desktop

VGW Virtual Genome Walking

Detects exons from assembled transcripts and assembles whole genome reads…

Detects exons from assembled transcripts and assembles whole genome reads against each exon. VGW allows user to fill gaps within genome assemblies. It can assemble flanking data and assemble exons.…

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LRSDAY
Desktop

LRSDAY Long-read Sequencing Data Analysis for Yeasts

Enables to create comprehensive annotations for various genomic features and…

Enables to create comprehensive annotations for various genomic features and produce chromosome-level end-to-end genome assembly. LRSDAY can be useful equally for genome assembly and annotation. It…

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Oyster River…
Desktop

Oyster River Protocol

Provides a multi-assembler and multi-kmer protocol. Oyster River Protocol…

Provides a multi-assembler and multi-kmer protocol. Oyster River Protocol furnishes a standardized set to perform transcriptome assembly. The software permits quality trimming, assembly with multiple…

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Chloroplast…
Desktop

Chloroplast assembly pipeline

Extracts chloroplast sequences from whole genome shotgun (WGS) sequences of…

Extracts chloroplast sequences from whole genome shotgun (WGS) sequences of plant species. Chloroplast assembly pipeline takes advantage of the known chloroplast structure and the resulting,…

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VirGenA
Desktop

VirGenA

Provides a reference-guided assembler of highly variable viral genomes. VirGenA…

Provides a reference-guided assembler of highly variable viral genomes. VirGenA is based on iterative mapping and de novo reassembling of highly variable regions. It is able to assemble consensus…

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ALPACA
Desktop

ALPACA ALLPAths and Celera Assembler

Uses low coverage, corrected long reads for contig formation, short reads for…

Uses low coverage, corrected long reads for contig formation, short reads for consensus accuracy, and long-insert pairs (indirectly) for scaffold formation. ALPACA exploits existing tools to assemble…

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FSG
Desktop

FSG Fast String Graph

Computes the string graph of a set R of reads with O(nmm) worst-case time…

Computes the string graph of a set R of reads with O(nmm) worst-case time complexity where n is the number of reads in R and m is the maximum read length. FSG is a tool for constructing a string…

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Faucet
Desktop

Faucet

Builds an assembly graph incrementally as each read is processed. Faucet is a…

Builds an assembly graph incrementally as each read is processed. Faucet is a 2-pass streaming algorithm for assembly graph construction. This algorithm is composed of an online phase and an offline…

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TULIP
Desktop

TULIP The Uncorrected Long-read Integration Process

Consists of two prototype scripts in Perl: tulipseed.perl and tulipbulb.perl.…

Consists of two prototype scripts in Perl: tulipseed.perl and tulipbulb.perl. The tulipseed script constructs the seed graph based on input SAM files and a set seed length, and outputs a simplified…

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IonGAP
Web

IonGAP

A publicly available web platform designed for the analysis of whole bacterial…

A publicly available web platform designed for the analysis of whole bacterial genomes by using Ion Torrent sequence data. Besides assembly, IonGAP integrates a variety of comparative genomics,…

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IVA
Desktop

IVA Iterative Virus Assembler

A de novo assembler designed to assemble virus genomes that have no repeat…

A de novo assembler designed to assemble virus genomes that have no repeat sequences, using Illumina read pairs sequenced from mixed populations at extremely high and variable depth. IVA produces…

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RAMPART
Desktop

RAMPART

A pipeline for creating multiple assemblies and a framework for analysing and…

A pipeline for creating multiple assemblies and a framework for analysing and comparing them. Rampart supports a variety of third-party tools for assembling, scaffolding and read error correction.…

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GAGE
Dataset

GAGE Genome Assembly Gold-standard Evaluations

Evaluates how genome assemblers compare on a spectrum of bacterial genomes…

Evaluates how genome assemblers compare on a spectrum of bacterial genomes sequenced by the newest sequencing technologies. GAGE-B is an evaluation of contiguity and accuracy of assemblies of…

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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PopPhyl
Desktop

PopPhyl

Allows transcriptome assembly, short read mapping and coding sequence…

Allows transcriptome assembly, short read mapping and coding sequence annotation of 454 and Illumina data sequences. The PopPhyl project aims at characterizing within- and between-species molecular…

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Mapsembler
Desktop

Mapsembler

Processes large datasets of reads on commodity hardware. Mapsembler checks the…

Processes large datasets of reads on commodity hardware. Mapsembler checks the presence of a known piece of information with a bounded number of substitutions in a set of reads. It provides pieces of…

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Unicycler
Desktop

Unicycler

Assembles bacterial genomes from a combination of short and long reads, which…

Assembles bacterial genomes from a combination of short and long reads, which produces assemblies that are accurate, complete and cost-effective. Unicycler builds an initial assembly graph from short…

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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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DBG2OLC
Desktop

DBG2OLC

Reduces the computational and sequencing requirements of 3GS assembly. DBG2OLC…

Reduces the computational and sequencing requirements of 3GS assembly. DBG2OLC combines different data types. This leads to both computation and cost efficiency. These advantages are gained from…

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HINGE
Desktop

HINGE

An assembler that achieves optimal repeat resolution by distinguishing repeats…

An assembler that achieves optimal repeat resolution by distinguishing repeats that can be resolved given the data from those that cannot. This is accomplished by adding "hinges" to reads…

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ABruijn…
Desktop

ABruijn assembler

Assembles long error-prone reads using de Bruijn graphs. While the running time…

Assembles long error-prone reads using de Bruijn graphs. While the running time of overlap-layout-consensus (OLC) assemblers is dominated by the overlap detection step, the running time of the…

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GATB
Desktop

GATB Genome Assembly & Analysis Tool Box

An open-source library dedicated to genome assembly and analysis to fasten the…

An open-source library dedicated to genome assembly and analysis to fasten the process of developing efficient software.

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Readjoiner
Desktop

Readjoiner

A method for the construction of a string graph from a set of sequencing reads.…

A method for the construction of a string graph from a set of sequencing reads. Readjoiner employs suffix sorting and scanning methods to compute suffix-prefix matches. Transitive edges are…

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HyDA-Vista
Desktop

HyDA-Vista

A genome assembler that uses homology information to choose a value of k for…

A genome assembler that uses homology information to choose a value of k for each read prior to the de Bruijn graph construction. The chosen k is optimal if there are no sequencing errors and the…

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Pilon
Desktop

Pilon

Corrects draft assemblies and calls sequence variants of multiple sizes,…

Corrects draft assemblies and calls sequence variants of multiple sizes, including very large insertions and deletions. Pilon improves draft genome assemblies by correcting bases, fixing…

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contiBAIT
Desktop

contiBAIT

Uses data from multiple single cells from the organism whose genome is to be…

Uses data from multiple single cells from the organism whose genome is to be assembled. contiBAIT can cluster unbridged contigs with each other into putative chromosomes, and order the contigs within…

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Arapan-S
Desktop

Arapan-S

Solves small genomes assembly. Arapan-S is a whole-genome assembly program…

Solves small genomes assembly. Arapan-S is a whole-genome assembly program dedicated to handling small genomes. It provides only one contig (along with the reverse complement of this contig) in many…

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liftoveR
Desktop

liftoveR

Incorporates multiple tools for alignment, including Bowtie (useful for…

Incorporates multiple tools for alignment, including Bowtie (useful for stringently aligning closely related sequences), Rsubread (useful for aligning related sequences while allowing gaps) and…

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GAML
Desktop

GAML Genome Assembly by Maximum Likelihood

Allows systematic combination of diverse sequencing datasets into a single…

Allows systematic combination of diverse sequencing datasets into a single assembly. We achieve this by searching for an assembly with the maximum likelihood in a probabilistic model capturing error…

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iWGS
Desktop

iWGS in silico Whole Genome Sequencer and Analyzer

An automated pipeline for guiding the choice of appropriate sequencing strategy…

An automated pipeline for guiding the choice of appropriate sequencing strategy and assembly protocols. iWGS seamlessly integrates the four key steps of a de novo genome sequencing project: data…

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DALIGNER
Desktop

DALIGNER

Finds all significant local alignments between reads. DALIGNER can also be used…

Finds all significant local alignments between reads. DALIGNER can also be used as a general read mapper and string to string comparison tool, as a “read” can now be a DNA sequence that is as…

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SMRT-Analysis
Desktop

SMRT-Analysis

Open-source bioinformatics software suite for sequence alignment, assembly,…

Open-source bioinformatics software suite for sequence alignment, assembly, variant detection, and base modification discovery.

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Newbler
Desktop

Newbler GS De novo assembler

A software package for de novo DNA sequence assembly.

A software package for de novo DNA sequence assembly.

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SHORTY
Desktop

SHORTY

Addresses the problem of higher margin of sequencing errors and other…

Addresses the problem of higher margin of sequencing errors and other artifacts. SHORTY is targeted for de novo assembly of microreads with mate pair information and sequencing errors. It has…

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Geneious
Desktop

Geneious

Proposes a powerful and comprehensive suite of next generation sequencing (NGS)…

Proposes a powerful and comprehensive suite of next generation sequencing (NGS) analysis tools. Through an intuitive and user-friendly interface, Geneious provides visual sequence alignment and…

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Gee Fu
Desktop

Gee Fu

Allows users to store and share of in-development assemblies and feature data.…

Allows users to store and share of in-development assemblies and feature data. Gee Fu is an open source software which intends to help in centralization and providing an easy data access to workers…

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fermi
Desktop

fermi

Assembles Illumina short read into unitigs while preserving most of information…

Assembles Illumina short read into unitigs while preserving most of information of the input reads. Fermi tool allows the assembly based variant calling can achieve a single-nucleotide polymorphism…

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COPE
Desktop

COPE Connecting Overlapped Pair-End

An efficient tool to connect overlapping pair-end reads using k-mer frequencies.

An efficient tool to connect overlapping pair-end reads using k-mer frequencies.

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CG-Pipeline
Desktop

CG-Pipeline

A tool for assembling genome sequence data and running feature prediction and…

A tool for assembling genome sequence data and running feature prediction and annotation tools on the assembly.

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SWAP-Assembler
Desktop

SWAP-Assembler Small World Asynchronous Parallel model-Assembler

A highly scalable assembler for processing massive sequencing data using…

A highly scalable assembler for processing massive sequencing data using thousands of cores, where SWAP is an acronym for Small World Asynchronous Parallel model. In SWAP-Assembler, two fundamental…

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NeatFreq
Desktop

NeatFreq

A software tool that reduces a data set to more uniform coverage by clustering…

A software tool that reduces a data set to more uniform coverage by clustering and selecting from reads binned by their median kmer frequency (RMKF) and uniqueness. The normalization of deep coverage…

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Lotus…
Web

Lotus japonicus genome assembly

A genome assembly constructed by a hybrid assembly integrating…

A genome assembly constructed by a hybrid assembly integrating Sanger-sequencing data from TAC/BAC clones and shotgun approaches with Illumina sequencing data to 40x genome coverage. A total of 132…

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TASR
Desktop

TASR Targeted Assembler of [short] Sequence Reads

A genomics application that allows hypothesis-based interrogation of genomic…

A genomics application that allows hypothesis-based interrogation of genomic regions (sequence targets) of interest. It only considers NGS reads for assembly that have overlap potential to input…

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AutoAssemblyD
Desktop

AutoAssemblyD

A graphical tool for genome assembly submission and remote management by…

A graphical tool for genome assembly submission and remote management by multiple assemblers through XML templates. AutoAssemblyD also facilitates assembly on remote devices through distributed…

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AMOS
Desktop

AMOS

Uses a collection of tools and class interfaces for the assembly of DNA reads.…

Uses a collection of tools and class interfaces for the assembly of DNA reads. AMOS includes a robust infrastructure, modular assembly pipelines, and tools for overlapping, consensus generation,…

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GapFiller
Desktop

GapFiller

A local assembler based on a seed-and-extend schema. Seed-and-extend assemblers…

A local assembler based on a seed-and-extend schema. Seed-and-extend assemblers repeatedly pick up a seed (it can be either a read or a previously assembled contig) and extend it using other reads.…

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SAM
Desktop

SAM Sequence Assembly Manager

Facilitates manipulation and coordination of analysis of sequence information.…

Facilitates manipulation and coordination of analysis of sequence information. SAM permits evaluation of the assembly quality and its progress. It can serve to visualize the clone tiling path…

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Assemblet
Desktop

Assemblet

Allows users to assemble bacteria’ antigenic variant sequences. Assemblet is…

Allows users to assemble bacteria’ antigenic variant sequences. Assemblet is a python short read assembler that can analyze sequencing reads of DNA that results from polymerase chain reaction (PCR)…

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V-pipe
Desktop

V-pipe

Allows users to study clinical applications of next generation sequencing (NGS)…

Allows users to study clinical applications of next generation sequencing (NGS) data.

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SeqMan NGen
Desktop

SeqMan NGen

Gathers any size genome. SeqMan NGen consists of sequence assembly software…

Gathers any size genome. SeqMan NGen consists of sequence assembly software that brings data from leading sequencing platforms. It supplies an interface that guides users through their editing and…

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IDBA
Desktop

IDBA Iterative De Bruijn graph de novo Assembler

Alleviates the difficulties in setting a correct k and the filtering threshold…

Alleviates the difficulties in setting a correct k and the filtering threshold m. IDBA can capture good contigs and these contigs can be made longer as k increases. It comports an initial filtering…

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Fermi-lite
Desktop

Fermi-lite

Permits to assemble short reads. Fermi-lite is able to capture heterozygous…

Permits to assemble short reads. Fermi-lite is able to capture heterozygous events and can be used to assemble diploid regions for variant calling tasks. It counts k-mer, estimates the k-mer…

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CLC Assembly…
Desktop

CLC Assembly Cell

Provides resources for mapping reads to a reference and de novo assembly of…

Provides resources for mapping reads to a reference and de novo assembly of next-generation sequencing (NGS) data. CLC Assembly Cell is a high-performance computing solution that includes utility…

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BWISE
Desktop

BWISE de Bruijn Workflow using Integral information of Short pair End reads

Provides an assembly of short pair end reads with the utilization of de Bruijn…

Provides an assembly of short pair end reads with the utilization of de Bruijn graphs. If the principal use is for paired reads of about 500-600bp (recommended library size), unpaired reads can also…