Atlas-SNP2 | Tool name | Atlas-SNP2 |
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| URL | http://www.hgsc.bcm.tmc.edu/cascade-tech-software_atlas_snp-ti.hgsc |
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| Important features | 1. Used for SNP discovery.
2. Supports data from roche 454 and illumina platform.
3. It also needs installation of SAMtools. |
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| Citations | Shen 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. |
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| Year of publication | 2010 |
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| Rank by usage frequency | 100 |
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| Comments | Requires installation of SAMTools in the path. |
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| Function | SNP discovery |
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| Category | Free, Downloadable |
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| License | |
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| Status | |
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| Input file format | SAM alignment files, reference in FASTA
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| Output file format | List of SNPs in tab limited form
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| Operating system | Unix |
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| Operating language | Ruby |
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| Platform | Illumina/Solexa, Roche 454 |
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| Maintained by | Baylor College of Medicine Human Genome Sequencing Center
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| Downloadable file format | |
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| Submission file format | |
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