Skip to main content

Table 1 Benchmark of SNP detection

From: Polymorphic edge detection (PED): two efficient methods of polymorphism detection from next-generation sequencing data

Method

ERR3063487

DRR054198

bwa + GATK

11,095 ± 60

154,105 ± 2761

k-mer

19,263 ± 22

187,177 ± 194

bidirectional

4149 ± 2

36,657 ± 309

  1. Short reads of Caenorhabditis elegans (ERR3063487, 100base, 13,549,514 pairs) and Oryza sativa L. cv. Koshihikari (DRR054198, 101base, 191,991,610 pairs) were analyzed by single computer with Intel Pentium G3250 @ 3.20GHz (2 cores) and 32Gb memory. Three times run averages with standard deviations of CPU user time (seconds) by time command were shown
Back to article page

BMC Bioinformatics

ISSN: 1471-2105

Contact us