read2SNPs 

[page edited on october, 14, 2013]

read2SNPs changes its name, call me now discoSnp!

read2snps name is already (almost) taken by a paper describing tool “reads2snp“. In order to avoid confusions, we changed its name for discoSnp: discovering SNPs. The name changes but the program remains the same. This page will thus not evolve anymore.

go to discoSnp

Description

Software read2SNPs is designed for extracting Single Nucleotide Polymorphism (SNP) from raw set(s) of reads obtained with Next Generation Sequencers (NGS).
Note that number of input read sets is not constrained, it can be one, two, or more. Note also that no other data as reference genome or annotations are needed.
The software is composed by two modules. First module, kissnp2, detects SNPs from read sets. A second module, kissreads, enhance the kissnp2 results by computing per read set  and for each found SNP i/ its mean read coverage and ii/ the (phred) quality of reads generating the polymorphism.

Citation

Paper in preparation.

Here is the kisnsp (1) publication:

P.Peterlongo, N.Schnel, N.Pisanti, M.-F. Sagot, V.Lacroix: Identifying SNPs without a reference genome by comparing raw reads,
proceedings of String Processing and Information Retrieval (SPIRE) 2010, Springer LNCS. In press.

Galaxy

  • read2SNPs can be used on the genouest galaxy server
  • read2SNPs can be integrated  in any galaxy instance using the GenOuest tool shed
    • Create a account: click on “you may create one“
    • Once account created and once you are logged, click on the “Symbiose” repository, then click on “read2snps”. From this repository you may download archives for installing read2snps on you galaxy instance.

Download

Please read and accept the License before use and diffusion.
Any feedback and comment is warmly encouraged.

Last version: read2SNPs_2.1.1.4

Logs:

  • 08/04/2013 read2SNPs_20130508: initial version
  • 09/04/2013 read2SNPs_2013_05_09_2: increases kissreads speed.
  • 11/04/2013 read2SNPs_2.0.5: checked the discovery of branching during bubble finding
  • 12/04/2013 read2SNPs_2.0.5.1: fixes a bug with the kissreads ranking function
  • 15/04/2013 read2SNPs_2.0.5.2: removes useless output and proposes a full pipeline with a use case
  • 16/04/2013 read2SNPs_2.0.5.3: fixes a (last ?) small bug with the ranking function & enhance the pipeline avoiding odd k values
  • 19/04/2013 read2SNPs_2.0.5.4: fixes an assymetrical filter on the branching. Now, without the -b option, none of the two extremities of a bubble should be branching (only right extremity was tested before)
  • 24/04/2013 read2SNPs_2.5.0.5: (minor) add the -x option = output only length of extensions, not extensions themselves.
  • 29/04/2013 read2SNPs_2.0.5.6: k-coverage is now applied by default into kissreads.
  • 14/05/2013 read2SNPs_2.0.5.7: fixes a (small) bug (branching closing kmer) that may lightly affect the results sensibility
  • 16/05/2013 read2SNPs_2.0.5.8: change the ranking function – improves the ranking for more than two data sets.
  • 15/07/2013 read2SNPs_2.1.0.0:
    • 1/ improves speed and memory (thank to  Salikhov, Kucherov and Sacomoto work)
    • 2/ adding post-treatment scripts
    • 3/ by default: keep the low complexity SNPs.
  • 29/07/2013 read2SNPs_2.1.1.0:
    • script run_read2SNPs.sh can now be called anywhere
    • bubbles are now of length 2k-1 instead of 2k+1 before extensions. This improves the precision/recall
  • 01/08/2013 read2SNPs_2.1.1.1
    • Bug fix (consequence of bubbles of length 2k-1)
  • 24/09/2013 read2SNPs_2.1.1.3
    • (2.1.1.2 not shown: modifications on codes with no consequence on the tool features)
    • Adding (by default in the pipeline) the -T option: extends each SNP using a contig, not only a unitig
  • 11/10/2013 read2SNPs_2.1.1.4
    • Parellelization of kissreads
    • readme is now also in .txt

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