Software

Software related to the project, developped within the Alcovna/Colib’read projects, or not.

  • KisSplice – A local transcriptome assembler for SNPs, indels and AS events
  • Mapsembler2 – targeted assembly and visualization
  • discoSnp++ – discovering Single Nucleotide Polymorphism (SNP) from raw set(s) of reads
  • TakeABreak – inversion breakpoints detection directly from raw NGS reads
  • Lordec – hybrid error correction program for long, PacBio reads
  • Commet – comparing and combining multiple metagenomic datasets
  • Short Read Connector – connect reads from (meta)-genomic dataset(s)
  • MindTheGap – detection and assembly of DNA insertion variants in NGS read datasets with respect to a reference genome
  • Leon – reference-free read compression
  • Minia – short-read assembler based on a de Bruijn graph

discoSnp++

[page edited on October, 27, 2016] – 2.2.10 version Tutorial A toturial can be followed from those slides demo_discosnp Description Software discoSnp++ is designed for discovering Single Nucleotide Polymorphism (SNP) and insertions/deletions (indels) from raw set(s) of reads obtained with Next Generation Sequencers (NGS). Note that number of input read sets is not constrained, it can …

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TakeABreak

[last edited on July, 7, 2015] Description TakeABreak is a tool that can detect inversion breakpoints directly from raw NGS reads, without the need of any reference genome and without de novo assembling the genomes. Its implementation has a very limited memory impact allowing its usage on common desktop computers and acceptable runtime (Illumina reads …

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Commet

Comparing and combining multiple metagenomic datasets [PAGE Created on July, 29 2014] Description: COMMET (“COmpare Multiple METagenomes”) provides a global similarity overview between all datasets of a large metagenomic project. Directly from non-assembled reads, all against all comparisons are performed through an efficient indexing strategy. Then, results are stored as bit vectors, a compressed representation …

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Compareads

Compareads is no more maintained. You can now use the new Commet software which does more and better than compareads. [PAGE UPDATED on July, 29 2014] Description: Compareads is a tool designed to extract similar reads between potentially huge metagenomic datasets (i.e., hundreds of millions reads per dataset) Download: The last Compareads release may be …

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Crac

See here: http://crac.gforge.inria.fr/

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Gk-Arrays

See here: http://crac.gforge.inria.fr/gkarrays/

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Kissplice

See here: http://kissplice.prabi.fr/

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MindTheGap

MindTheGap is a tool to detect and assemble insertion variants of any size and any type, by comparison with a reference genome. For download and more details, see the web page : https://gatb.inria.fr/software/mind-the-gap/ Citation Guillaume Rizk, Anaïs Gouin, Rayan Chikhi and Claire Lemaitre. MindTheGap : integrated detection and assembly of short and long insertions. Bioinformatics …

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Minia

See here: http://minia.genouest.org/

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Screen Shot 2014-08-12 at 15.15.44

Mapsembler2

[page edited on Octobber, 31th, 2014] Mapsembler2 description and possible usages: Mapsembler2 is a targeted assembly software. It takes as input any number of NGS raw read set(s) (fasta or fastq, gzipped or not) and a set of input sequences (starters). For each starter, Mapsembler2 outputs its sequence neighborhood as a linear sequence or as …

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