Author's posts

Workshop Colib’read – Program Online

The Colib’read workshop program is now online on this page http://gdr-bim.cnrs.fr/colibread/program/. We remind you that the attendance is free but ***registration is mandatory*** see website: http://gdr-bim.cnrs.fr/colibread/. Note that space is limited, and registration will be taken in the order received. — WHAT — Calling biological information from raw reads and long reads correction. All methods …

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Short Read Connector presentation

Short Read Connector was published and presented during the Prague Stringology Conference 2016. Slides available from Pierre’s presentation page.

New discoSnp release

A new discoSnp release is available. The VCF creation had been improved. A small bug had been fixed and the computation time is divided by approximately a factor 3. Check this new release 2.2.9 here

Workshop colib’read – November 7,8 2016

The colib’read group (http://colibread.inria.fr/) organises a workshop which aim is to present tools and results obtained for “calling biological information from raw reads”. The tools developed by the group are efficient both in terms of memory and computing time. Most of these tools are reference-free and assembly-free, and thus give the possibility to analyse reads …

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Using discoSnp for finding SNPs in pea read sets, paper published in BMC Genomics

Gilles Boutet, Susete Alves Carvalho, Matthieu Falque, Pierre Peterlongo, Emeline Lhuillier, et al.. SNP discovery and genetic mapping using genotyping by sequencing of whole genome genomic DNA from a pea RIL population. BMC Genomics, 2016, 17 (1), pp.121. <10.1186/s12864-016-2447-2>. <hal-01275696>

Paper Colib’read on galaxy published in GigaScience

Yvan Le Bras, Olivier Collin, Cyril Monjeaud, Vincent Lacroix, Eric Rivals, et al.. Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads. GigaScience, BioMed Central, 2016, 5 (1), <10.1186/s13742-015-0105-2>. <hal-01280238>

New discoSnp++ release

New discoSnp++ released (version 2.2.1). Fixes not-so-minor bugs and improves the VCF creation. http://colibread.inria.fr/software/discosnp/

discoSnp++2.2.0 released

A new discoSnp++ release is available. http://colibread.inria.fr/software/discosnp/ Existing features in a few words Detect SNPs and indels from raw read set(s), without the need of a reference genome. Provides genotyping and ranking Generates a fasta file of variant predictions containing a micro-assembly of the variant left and rigth neighbors Generates a VCF of predicted variants …

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Galaxy Docker repository for metagenomics

Björn Grüning developped a  Galaxy Docker repository for metagenomics including commet : https://github.com/bgruening/galaxy-metagenomics

DiscoSnp++ now genotypes results and provides a VCF file

From version 2.1.2, discoSnp++ includes several new features as the usage of paired reads, the creation of a genotype or the production of a VCF with or without the use of a reference genome. Info and downloads : discoSnp++ page