AGSNP is an annotation-based, genome-wide SNP discovery pipeline package using NGS data for large and complex genomes without a reference genome sequence. Roche 454 shotgun reads with low genome coverage of one individual are annotated in order to distinguish single-copy sequences and repeat junctions from repetitive sequences and sequences shared by paralogous genes. Multiple genome equivalents of shotgun reads of another individual generated with SOLiD or Solexa are then mapped to the annotated Roche 454 reads to identify putative SNPs. The pipeline is suitable for SNP discovery in genomic libraries of complex genomes and does not require a reference genome sequence. The pipeline is applicable to all current NGS platforms, provided that at least one of them generates relatively long reads.
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Genome-wide SNP discovery in walnut with an AGSNP pipeline updated for SNP discovery in allogamous organisms.
You FM, Deal KR, Wang J, Britton MT, Fass JN, Lin D, Dandekar A, Leslie CA, Aradhya M, Luo MC, Dvorak J.
BMC Genomics. 2012 Jul 31;13(1):354.
You FM, Huo N, Deal KR, Gu YQ, Luo MC, McGuire PE, Dvorak J, Anderson OD.
Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence.
BMC Genomics, 2011, 12(1):59.