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Table 8 Percent of 100,000 ancient horse DNA reads (SRR111892) of length 76 bp mapped to the horse genome Equus_caballus EquCab2 (GCA_000002305.1) and human reference genome

From: MaxSSmap: a GPU program for mapping divergent short reads to genomes with the maximum scoring subsequence

Horse genome
BWA NextGenMap NextGenMap+ NextGenMap+ NextGenMap+
   MaxSSmap_fast MaxSSmap CUDASW++
2.2 16 20.5 23.1 26 (estimated)
  Time in minutes to map reads
0.6 2.4 1609.6 2836 14820 (estimated)
Human genome
BWA NextGenMap NextGenMap+ NextGenMap+ NextGenMap+
   MaxSSmap_fast MaxSSmap CUDASW++
0.16 14 18.6 21 NA
  Time in minutes to map reads
0.82 2.9 2375.5 4108 NA
  1. We ran NextGenMap+CUDA-SW++ for a maximum of 168 hours and estimated the time to align all rejected reads. Also shown is time in minutes.
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BMC Genomics

ISSN: 1471-2164

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