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kisSnp tool [OBSOLETE].

by Pierre Peterlongo on June 10th, 2010

Citation

If you use this software please cite:

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.

Download and install. [EDIT 29/03/2011: DO NOT USE THIS VERSION ANYMORE, IT'S REPLACED BY kisSnp written in C, lighter and faster.]

NEW VERSION IS AVAILABLE HERE: kisSnp page.

See upcoming post

zip file containing the mouth finding algorithm (kisSnpSNP) and the read check algorithm (kisSnpCheckReads) : kisSnp_suite

unzip the kisSnp_suite.zip file.

Usage

kisSnp

java -jar kisSnp reads1.fasta reads2.fasta k delta name [limit]

with

read1.fasta: a fasta file containing all reads of the first sequence
read2.fasta: a fasta file containing all reads of the second sequence
k: the length of the k-mers
delta: variability authorized during mouth extention
name: output prefix name
limit: stop the computation after finding limit SNP (opitional)

kisSnpCheckReads

java -jar ../kisSnpCheckReads.jar reads1.fasta reads2.fasta  mouth_file_A mouth_file_B kmer_length minoverlap [verbose]

with:

read1.fasta: a fasta file containing all reads of the first sequence
read2.fasta: a fasta file containing all reads of the second sequence

mouth_file_A: the upper lips of the mouths found by kisSnp

mouth_file_B: the lower lips of the mouths found by kisSnp

kmer_length: lengh of kmers used for linking lips to reads (10 is a good value)

minoverlap: minimal overlap requested between two reads to be coherents

verbose or v: prints coherent reads with lips, else only prints:

number of mouths tested           number of mouths read coherents       number of mouths non read coherents

 

Example:

  1. download and unzip reads_example
  2. find putative SNPs by running  kisSnp: “java -jar ../kisSnp.jar reads1.fna reads2.fna 22 30 reads1vs2″ (k=22, delta=30)
    • Provides two files: reads1vs2_22_30_A.out and reads1vs2_22_30_B.out.
    • i th line of each file correspond to a lip of SNP mouth.
  3. check read coherence: java -jar ../kisSnpCheckReads.jar reads1.fna reads2.fna reads1vs2_22_30_A.out reads1vs2_22_30_B.out 10 2 v (use kmers of length 10 for finding reads and minimal overlap of length 2 between two reads).

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