Sep 27

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 are reference free.

— HOW —
The workshop is composed of overview and practical talks, of success stories (bioanalyses results), of tools demonstrations and of interactive discussions.

— WHEN —
November 7,8 2016

— LANGUAGE —
English

— WHERE —
Institut Curie – Amphithéâtre Constant Burg  12, Rue Lhomond 75005 Pari

— REGISTRATION —
The workshop attendance is free but ***registration is mandatory*** (see website)

— WEB SITE —
http://gdr-bim.cnrs.fr/colibread/

Sep 15

Short Read Connector presentation

Short Read Connector was published and presented during the Prague Stringology Conference 2016.

Slides available from Pierre’s presentation page.

Jun 27

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

Jun 16

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 without a reference genome or without performing de novo assembly.
The methods we developed can readily be used to find variants in the context of non-model species, where no (good) reference genome is available, but we also would like to promote their use in the context of model species, especially in disease conditions.

Presentations will include a taste of algorithmic and will show some applications and results obtained using our proposed tools, such as kissplice [1], discoSnp [2] or Lordec [3]. We will also propose some interactive tool demonstrations and the program will include time for discussions.

[1] http://kissplice.prabi.fr
[2] http://colibread.inria.fr/software/discosnp
[3] http://www.atgc-montpellier.fr/lordec/

— WHEN —
November 7,8 2016

— WHERE —
Institut Curie – Amphithéâtre Constant Burg  12, Rue Lhomond 75005 Pari

— REGISTATION —
The workshop attendance is free but ***registration is mandatory*** (see website)

— WEB SITE —
http://gdr-bim.cnrs.fr/colibread/

Mar 04

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>https://hal.inria.fr/hal-01275696/file/12864_2016_Article_2447.pdf BibTex

Mar 04

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>https://hal.inria.fr/hal-01280238/file/colibread_galaxy.pdf BibTex

Oct 05

New discoSnp++ release

New discoSnp++ released (version 2.2.1). Fixes not-so-minor bugs and improves the VCF creation.

Jul 20

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
    • Without a reference: no informative prediction locus
    • Providing a reference sequence: map predictions. The VCF contains mapping information (locus, multiple matches, …)
  • Fast, low memory footprint, easy to use.

New features

  • New input format (using file of files)
    • Easier to deal with paired datasets
    • Easier to simulate file concatenation
  • The reference can also be used for calling predictions (not only for mapping them)
  • The coverage thresholds can be
    • set separately for each read set
    • and/or automatically detected for each set

Any comment / remark positive or not is still warmly welcome on the biostar forum

Jun 12

Galaxy Docker repository for metagenomics

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

url

Mar 25

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