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A compilation and categorization of next-generation sequencing resources

Atlas-SNP2

Tool nameAtlas-SNP2
URLhttp://www.hgsc.bcm.tmc.edu/cascade-tech-software_atlas_snp-ti.hgsc
Important features1. Used for SNP discovery. 2. Supports data from roche 454 and illumina platform. 3. It also needs installation of SAMtools.
CitationsShen Y, Wan Z, Coarfa C, Drabek R, Chen L, Ostrowski EA, Liu Y, Weinstock GM, Wheeler DA, Gibbs RA, Yu F. A SNP discovery method to assess variant allele probability from next-generation resequencing data. Genome Res. 2010 Feb;20(2):273-80. Epub 2009 Dec 17. PubMed PMID: 20019143; PubMed Central PMCID: PMC2813483.
Year of publication2010
Rank by usage frequency100
CommentsRequires installation of SAMTools in the path.
FunctionSNP discovery
CategoryFree, Downloadable
License
Status
Input file formatSAM alignment files, reference in FASTA
Output file formatList of SNPs in tab limited form
Operating systemUnix
Operating languageRuby
PlatformIllumina/Solexa, Roche 454
Maintained byBaylor College of Medicine Human Genome Sequencing Center
Downloadable file format
Submission file format

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