Introduction

SOAPsnp is a member of the Short Oligonucleotide Analysis Package (SOAP). Despite its name, the program is a resequencing utility that can assemble consensus sequence for the genome of a newly sequenced individual based on the alignment of the raw sequencing reads on the known reference. The SNPs can then be identified on the consensus sequence through the comparison with the reference. In the first Asian genome re-sequencing project, evaluation of SOAPsnp result on Illumina HapMap 1M BeadChip Duo genotyping sites showed great accuracy. Over 99% of the genotyping sites were covered at over 99.9% consistency. Further PCR plus Sanger sequencing of the inconsistent SNP sites confirmed majority of the SOAPsnp results.

For more information, visit the SOAPsnp official website.

Programming language: C++

Brief description: A member of the Short Oligonucleotide Analysis Package (SOAP).

Open source license: custom open source license

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