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Listes des outils NGS au sein de la plateforme Migale

Version imprimable
Voici la liste des outils disponibles au sein de la plateforme Migale et pouvant être utilisés pour faire des NGS :
  • abyss : ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.

  • amos : AMOS: A Modular Open-Source Assembler

  • art : ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms: Illumina's Solexa, Roche's 454 and Applied Biosystems' SOLiD. ART can be used to test or benchmark a variety of method or tools for next-generation sequencing data analysis, including read alignment, de novo assembly, SNP and structure variation discovery. ART was used as a primary tool for the simulation study of the 1000 Genomes Project . ART is implemented in C++ with optimized algorithms and is highly efficient in read simulation. ART outputs reads in the FASTQ format, and alignments in the ALN format. ART can also generate alignments in the SAM alignment or UCSC BED file format.

  • bedtools : The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by "streaming" several BEDTools together. The following are examples of common questions that one can address with BEDTools.

  • bfast : BFAST : Blat-like Fast Accurate Search Tool BFAST facilitates the fast and accurate mapping of short reads to reference sequences. Some advantages of BFAST include: * Speed: enables billions of short reads to be mapped quickly. * Accuracy: A priori probabilities for mapping reads with defined set of variants. * An easy way to measurably tune accuracy at the expense of speed.

  • bowtie : Bowtie is an ultrafast, memory-efficient short read aligner. It 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 memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).

  • bowtie2 : Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.

  • bwa : BWA is a fast light-weighted tool that aligns short sequences to a sequence database, such as the human reference genome. By default, BWA finds an alignment within edit distance 2 to the query sequence, except for disallowing gaps close to the end of the query. It can also be tuned to find a fraction of longer gaps at the cost of speed and of more false alignments.

  • cd-hit-454 : The 454 pyrosequencing reads contains artificially duplicates, which might lead to misleading conclusions. cdhit-454 is a fast program to identify exact and nearly identical duplicates, the reads begin at the same position but may vary in length or bear mismatches. cdhit-454 can process a dataset in ~10 minutes. it also provides a consensus sequence for each group of duplicates.

  • Celera Assembler (wgs) : Celera Assembler is scientific software for DNA research. It can reconstruct long sequences of genomic DNA from the fragmentary data produced by whole-genome shotgun sequencing. The Celera Assembler is mature, efficient, open-source software written mostly in C for unix operating systems.

  • CNVnator : CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing.

  • corona : The SOLiD System Analysis Pipeline Tool (Corona Lite) is an off-instrument SOLiD data analysis software package. It supports functionality for mapping color space reads to large or small genomes, pairing for mate-pair runs, SNP calling and generating consensus sequences.

  • cufflinks : Cufflinks assembles transcripts and estimates their abundances in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one.

  • cutadapt : cutadapt is used to remove adapter sequences from high-throughput sequencing data. This is usually necessary when the read length of the sequencing machine is longer than the molecule that is sequenced, for example when sequencing microRNAs.

  • delly : DELLY is an integrated structural variant prediction method that can detect deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome.

  • dwgsim : Whole genome simulation can be performed with dwgsim. dwgsim is based off of wgsim found in SAMtools written by Heng Li. It was modified to handle ABI SOLiD data, as well as various assumptions about aligners and positions of indels. The documentation below is for the latest dwgsim (not DNAA) release.

  • EDGE-pro : EDGE-pro, Estimated Degree of Gene Expression in PROkaryots is an efficient software system to estimate gene expression levels in prokaryotic genomes from RNA-seq data. EDGE-pro uses Bowtie2 for alignment and then estimates expression directly from the alignment results. EDGE-pro includes routines to assign reads aligning to overlapping gene regions accurately. 15% or more of bacterial genes overlap other genes, making this a significant problem for bacterial RNA-seq, one that is generally ignored by programs designed for eukaryotic RNA-seq experiments.

  • FastQC : FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.

  • Fastq_Screen : Fastq screen is a simple application which allows you to search a large sequence dataset against a panel of different databases to build up a picture of where the sequences in your data originate. It was built as a QC check for sequencing pipelines but may also have uses in metagenomics studies where mixed samples are expected. Although the program wasn't built with any particular technology in mind it is probably only really suitable for processing short reads due to the use of bowtie/bowtie2 as the searching application. The program generates both text and graphical output to tell you what proportion of your library was able to map, either uniquely or in more than one location, against each of the databases in your search set.

  • FLASH : FLASH, Fast Length Adjustment of SHort reads, is a very accurate fast tool to merge paired-end reads from fragments that are shorter than twice the length of reads. The extended length of reads has a significant positive impact on improvement of genome assemblies.

  • flux-simulator : The Flux Simulator aims at modeling RNA-Seq experiments in silico: sequencing reads are produced from a reference genome according annotated transcripts. The simulation pipeline models different steps as modules, each with a minimal set of parameters that can be estimated by experimental parameters. The first step is-in fact-a transcriptome simulator. Subsequently, common sources of systematic bias in the abundance and distribution of produced reads are simulated by in silico library preparation and sequencing.

  • GASSST : GASSST : Global Alignment Short Sequence Search Tool * GASSST finds global alignments of short DNA sequences against large DNA banks. * GASSST strong point is its ability to perform fast gapped alignments. * It works well for both short and longer reads. It currently has been tested for reads up to 500bp. * The software is freely available for download under the CECILL version 2 License.

  • GEM : The GEM library (Also home to: The GEM mapper, The GEM RNA mapper, The GEM mappability, and others). Next-generation sequencing platforms (Illumina/Solexa, ABI/SOLiD, etc.) call for powerful and very optimized tools to index/analyze huge genomes. The GEM library strives to be a true "next-generation" tool for handling any kind of sequence data, offering state-of-the-art algorithms and data structures specifically tailored to this demanding task. At the moment, efficient indexing and searching algorithms based on the Burrows-Wheeler transform (BWT) have been implemented.

  • GMAP/GSNAP : GMAP (genomic mapping and alignment program for mRNA and EST sequences): gmap, a standalone program for mapping and aligning cDNA sequences to a genome. The program maps and aligns a single sequence with minimal startup time and memory requirements, and provides fast batch processing of large sequence sets. The program generates accurate gene structures, even in the presence of substantial polymorphisms and sequence errors, without using probabilistic splice site models. GSNAP (Genomic Short-read Nucleotide Alignment Program): GSNAP implements computational methods for fast detection of complex variants and splicing in short reads, based on a successively constrained search process of merging and filtering position lists from a genomic index. It can align both single- and paired-end reads as short as 14 nt and of arbitrarily long length. It can detect short- and long-distance splicing, including interchromosomal splicing, in individual reads, using probabilistic models or a database of known splice sites.

  • goby : Goby is a next-gen data management framework designed to facilitate the implementation of efficient next-gen data analysis pipelines. Goby provides compressed file formats that are time and space efficient. It also provides a few utilities that support the most common secondary data analyses

  • ICORN : iCORN (iterative correction of reference nucleotides) can correct genome sequences with short reads. Reads are mapped iteratively against the genome sequences, so far by SSAHA. Discrepancies between the multiple alignments of the mapping reads and reference are corrected, if by the correction the amount of perfect mapping reads doesn't decrease.

  • Illumina CASAVA-1.8 FASTQ Filter : The recent version of Illumina's CASAVA pipeline (Version 1.8) produces FASTQ files with both reads that pass filtering and reads that don't. The new READ-ID (the @ line) contains many new fields, one of them indicates whether the read is filtered or not. This program can filter FASTQ files produced by CASAVA 1.8, and keep/discard reads based on this filter flag.

  • inGAP : This is a novel mining pipeline (2009), Integrative Next-generation Genome Analysis Pipeline (inGAP), guided by a Bayesian principle to detect single nucleotide polymorphisms (SNPs), insertion/deletions (indels) by comparing high-throughput pyrosequencing reads with a reference genome of related organisms. inGAP can be applied to the mapping of both Roche/454 and Illumina reads with no restriction of read length.

  • jellyfish : JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the "jellyfish dump" command. See the documentation below for more details.

  • kraken : raken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.

  • macs : Next generation parallel sequencing technologies made chromatin immunoprecipitation followed by sequencing (ChIP-Seq) a popular strategy to study genome-wide protein-DNA interactions, while creating challenges for analysis algorithms. We present Model-based Analysis of ChIP-Seq (MACS) on short reads sequencers such as Genome Analyzer (Illumina / Solexa). MACS empirically models the length of the sequenced ChIP fragments, which tends to be shorter than sonication or library construction size estimates, and uses it to improve the spatial resolution of predicted binding sites. MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome sequence, allowing for more sensitive and robust prediction. MACS compares favorably to existing ChIP-Seq peak-finding algorithms, is publicly available open source, and can be used for ChIP-Seq with or without control samples.

  • mapsembler : Mapsembler is a targeted assembly software. It takes as input a set of NGS raw reads and a set of input sequences (starters). It first determines if each starter is read-coherent, e.g. whether reads confirm the presence of each starter in the original sequence. Then for each read-coherent starter, Mapsembler outputs its sequence neighborhood as a linear sequence or as a graph, depending on the user choice.

  • MapSplice : MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery MapSplice est un algorithme de seconde génération de détection de sites d'épissage alternatifs. Son objectif est de détecter les sites d'épissage de façon sensible et spécifique en maintenant une bonne efficacité au niveau CPU et mémoire. MapSplice peut être appliqué aux reads courts (>75 pb) et long (75 pb). Il ne dépend ni des caractéristiques du site d'épissage ni de la longueur de l'intron, par conséquent, il peut détecter de nouveaux sites canoniques et non-canoniques d'épissage. MapSplice s'appuie sur la qualité et la diversité d'alignements des reads pour augmenter la précision de détection des sites d'épissage.

  • maq : Maq is a software that builds mapping assemblies from short reads generated by the next-generation sequencing machines. It is particularly designed for Illumina-Solexa 1G Genetic Analyzer, and has a preliminary functionality to handle AB SOLiD data.

  • metagene : Gene Finding Program for Metagenomics MetaGene predicts prokaryotic genes on anonymous genomic sequences. Fragmented sequences (longer than 100 bp) can be accepted.

  • MetaGeneAnnotator : Version améliorée du programe d'annotation de données métagénomiques Metagene. Prediction de genes procaryotes à partir d'un génome ou d'un set de génomes anonymes. Particulierement adapté aux analyses métagénomiques.

  • minia : Minia is a short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. The output of Minia is a set of contigs. Minia produces results of similar contiguity and accuracy to other de Bruijn assemblers (e.g. Velvet).

  • mira : MIRA is a Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina. It can perform Hybrid de-novo assemblies as well as SNP and mutations discovery for mapping assemblies.

  • MIReNA :

  • mmseq : MMSEQ: haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads pipeline The flowchart to the right depicts the MMSEQ pipeline for obtaining expression estimates from RNA-seq data. There are two routes, with starting points labelled A and B. Route A is quite fast and straightforward to run and uses pre-existing transcript sequences for alignment. Route B requires more time, as it involves the creation of custom transcript sequences based on the data.

  • MMSEQ : MMSEQ: haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads

  • MOCAT : MOCAT is a package for analyzing metagenomics datasets. Currently MOCAT supports Illumina single- and paired-end reads in raw FastQ format.

  • MOSAIK assembler : MOSAIK is a reference-guided assembler comprising of four main modular programs: * MosaikBuild * MosaikAligner * MosaikSort * MosaikAssembler. MosaikBuild converts various sequence formats into Mosaik’s native read format. MosaikAligner pairwise aligns each read to a specified series of reference sequences. MosaikSort resolves paired-end reads and sorts the alignments by the reference sequence coordinates. Finally, MosaikAssembler parses the sorted alignment archive and produces a multiple sequence alignment which is then saved into an assembly file format.

  • MPscan : MPscan: fast localisation of multiple reads in genomes

  • mrFAST : mrFAST is a read mapper that is designed to map short reads to reference genome with a special emphasis on the discovery of structural variation and segmental duplications. mrFAST maps short reads with respect to user defined error threshold, including indels up to 4+4 bp. This manual, describes how to choose the parameters and tune mrFAST with respect to the library settings. mrFAST is designed to find 'all' mappings for a given set of reads, however it can return one "best" map location if the relevant parameter is invoked. NOTE: mrFAST is developed for Illumina, thus requires all reads to be at the same length. For paired-end reads, lengths of mates may be different from each other, but each "side" should have a uniform length.

  • mrsFAST : mrsFAST is a cache oblivious mapper that is designed to map short reads to reference genome. mrsFAST maps short reads with respect to user defined error threshold. In this manual, we will show how to choose the parameters and tune mrsFAST with respect to the library settings. mrsFAST is designed to find 'all' the mappings for a given set of reads.

  • nesoni : Nesoni focusses on analysing the alignment of reads to a reference genome. We use the SHRiMP read aligner, as it is able to detect small insertions and deletions in addition to SNPs. Nesoni can call a consensus of read alignments, taking care to indicate ambiguity. This can then be used in various ways: to determine the protein level changes resulting from SNPs and indels, to find differences between multiple strains, or to produce n-way comparison data suitable for phylogenetic analysis in SplitsTree4. Alternatively, the raw counts of bases at each position in the reference seen in two different sequenced strains can compared using Fisher's Exact Test.

  • newbler : Newbler is a package of three data analysis applications made by Roche 454 : the GS De Novo Assembler (with or without contig scaffolding using Paired End reads), the GS Reference Mapper, and the GS Amplicon Variant Analyzer (AVA). An additional application, the GS Run Browser, is an interactive Run browser/ troubleshooting tool which displays graphically the images, some intermediate data, and various output metrics from a sequencing Run. The software package also includes the SFF Tools commands for handling and using the data files (called Standard Flowgram Format or SFF files) that hold the sequencing trace data.

  • NGSToolsMIG : Tools developed in MIG laboratory to help in the process of Next generation Sequencing Data analysis : quality control, mapping, assembly, global statistics, etc. ///////// adaptiveTrim.pl ///////// alignmentStatistics.pl ///////// contigsExtractionOnLength.pl ///////// fastqQualityConverter.pl ///////// gbk2Fasta.pl ///////// globalTrim.pl ///////// multiFasta2Fasta.pl ///////// show2Fasta.pl ///////// unmappedReadsExtraction.pl ///////// (Cf. Doc)

  • novoalign : Novoalign is an aligner for single-ended and paired-end reads from the Illumina Genome Analyser. Novoalign finds global optimum alignments using full Needleman-Wunsch algorithm with affine gap penalties.

  • prinseq : PRINSEQ CAN BE USED TO FILTER, REFORMAT, OR TRIM YOUR GENOMIC AND METAGENOMIC SEQUENCE DATA. IT GENERATES SUMMARY STATISTICS OF YOUR $ GRAPHICAL AND TABULAR FORMAT.

  • ProbeMatch : ProbeMatch is a sequence alignment program that finds sequence alignments for short DNA sequences ( 36-50 bp ). Unlike other programs such as eland and soap that perform ungapped alignment allowing up to 2 substitution, Probematch performs *gapped* alignment, allowing up to 3 errors including substitution, insertion, and deletion.

  • Quake : Quake is a package to correct substitution sequencing errors in experiments with deep coverage (e.g. >15X), specifically intended for Illumina sequencing reads. Quake adopts the k-mer error correction framework, first introduced by the EULER genome assembly package. Unlike EULER and similar progams, Quake utilizes a robust mixture model of erroneous and genuine k-mer distributions to determine where errors are located. Then Quake uses read quality values and learns the nucleotide to nucleotide error rates to determine what types of errors are most likely. This leads to more corrections and greater accuracy, especially with respect to avoiding mis-corrections, which create false sequence unsimilar to anything in the original genome sequence from which the read was taken.

  • quip : Quip compresses next-generation sequencing data with extreme prejudice. It supports input and output in the FASTQ and SAM/BAM formats, compressing large datasets to as little as 15% of their original size.

  • ray : Ray is a parallel de novo genome assembler that utilises the message-passing interface everywhere and is implemented using peer-to-peer communication.

  • ReAS : ReAS: Recovery of Ancestral Sequences for Transposable Elements from the Unassembled Reads of a Whole Genome Shotgun

  • reptile : Reptile is a software developed in C++ for correcting sequencing errors in short reads from next-gen sequencing platforms.

  • rna2map : The SOLiD System Small RNA Analysis Pipeline Tool (RNA2MAP) can be used to perform whole genome analysis of color space RNA library reads. It consists of three major procedures: filtering, matching against miRBase sequences (Sanger), and matching against a reference genome.

  • RUM : RUM is an alignment, junction calling, and feature quantification pipeline specifically designed for Illumina RNA-Seq data.

  • samToFastq : Extracts read sequences and qualities from the input SAM/BAM file and writes them into the output file in Sanger fastq format. In the RC mode (default is True), if the read is aligned and the alignment is to the reverse strand on the genome, the read's sequence from input SAM file will be reverse-complemented prior to writing it to fastq in order restore correctly the original read sequence as it was generated by the sequencer.

  • SAMtools : SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

  • seqmap : SeqMap is a tool for mapping large amount of oligonucleotide to the genome. It is designed for finding all the places in a genome where an oligonucleotide could potentially come from. SeqMap can efficiently map as many as dozens of millions of short sequences to a genome of several billions of nucleotides. While doing the mapping, several mutations as well as insertions/deletions of the nucleotide bases in the sequences can be tolerated and furthermore detected. Various input and output formats are supported, as well as many command line options for tuning almost every steps in the mapping process.

  • seqtk : Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.

  • sickle : sickle - A windowed adaptive trimming tool for FASTQ files using quality

  • snap : SNAP is a new sequence aligner that is 10-100x faster and simultaneously more accurate than existing tools like BWA, Bowtie2 and SOAP2. It runs on commodity x86 processors, and supports a rich error model that lets it cheaply match reads with more differences from the reference than other tools. This gives SNAP up to 2x lower error rates than existing tools and lets it match larger mutations that they may miss.

  • soap : SOAPaligner/soap2 is a member of the SOAP (Short Oligonucleotide Analysis Package). It is an updated version of SOAP software for short oligonucleotide alignment. The new program features in super fast and accurate alignment for huge amounts of short reads generated by Illumina/Solexa Genome Analyzer. Compared to soap v1, it is one order of magnitude faster. It require only 2 minutes aligning one million single-end reads onto the human reference genome. Another remarkable improvement of SOAPaligner is that it now supports a wide range of the read length.

  • soap.coverage : Utility for SOAP - soap.coverage can calculate sequencing coverage or physical coverage as well as duplication rate and details of specific block for each segments and whole genome by using SOAP, BLAT, BLAST, BlastZ, mum- mer and MAQ aligement results with multi-thread.

  • SOAPdenovo : SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way.

  • SolexaQA : SolexaQA is a Perl-based software package that calculates quality statistics and creates visual representations of data quality from FASTQ files generated by Illumina second-generation sequencing technology (“Solexa”).

  • SPAdes : SPAdes is a de Bruijn graph based assembler. It integrates a read error corrector, a multiple kmer De Bruijn graph assembler, an assembly merger, a scaffoler and a repeat resolver.

  • ssaha2 : SSAHA (Sequence Search and Alignment by Hashing Algorithm) is an algorithm for very fast matching and alignment of DNA sequences. It achieves its fast search speed by encoding sequence information in a perfect hash function.

  • ssake : SSAKE is a genomics application for assembling millions of very short DNA sequences.sIt is an easy-to-use, robust, reliable and tractable clustering algorithm for very short sequence reads, such as those generated by Illumina Ltd.

  • sspace : SSPACE is not a de novo assembler, it is used after a preassembled run. SSPACE is a script to extend and scaffold preassembled contigs using a number of mate pairs or paired-end libraries. It uses Bowtie to map all the reads to the pre-assembled contigs. Unmapped reads are used for extending, if desired, the pre-assembled contigs with the SSAKE assembler. Again Bowtie is used to map the reads to the extended contigs. Positions and orientation of the reads are stored and used for scaffolding. If both reads of a pair are found within the allowed distance, they are used for scaffolding to determine the orientation, contig pairing and ordering of the contigs.

  • stacks : Stacks is a software pipeline for building loci out of a set of short-read sequenced samples. Stacks was developed for the purpose of building genetic maps from RAD-Tag Illumina sequence data, but can also be readily applied to population studies, and phylogeography.

  • tablet : Tablet is a lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments.

  • tagdust : TagDust is a program to eliminate artifactual reads from next-generation sequencing data sets.

  • tophat : TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.

  • Trimmomatic : Trimmomatic: A flexible read trimming tool for Illumina NGS data Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.

  • Trinity : RNA-Seq De novo Assembly Using Trinity Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads.

  • vcake : VCAKE is a genetic sequence assembler capable of assembling millions of small nucleotide reads even in the presence of sequencing error. This software is currently geared towards de novo assembly of Illumina's Solexa Sequencing data.

  • velvet : Sequence assembler for very short reads. Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.