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Table 10 Assembly reconciliation tools performances on human chromosome 14.

From: GAM-NGS: genomic assemblies merger for next generation sequencing

Tool User (CPU) time Wall clock time
Allpaths-LG + CABOG
GAM-NGS 4h 24' 59" + 1h 14' 41" 45' 56" + 18' 16"
GAA 452h 18' 14h 16' 4"
CABOG + Allpaths-LG
GAM-NGS 4h 24' 59" + 1h 12' 35" 45' 56" + 19' 21"
GAA 467h 40' 13h 44' 58'
  1. In GAM-NGS's entries the first value indicates the time spent in alignment phase, while the second one is GAM-NGS's run time. Due to the size of the assemblies, we parallelized BLAT's execution to get GAA's output in a reasonable time. ZORRO results are not shown due to the fact that the tool cannot run in parallel and, after more than a week of computation, was still not able to provide an output.
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BMC Bioinformatics

ISSN: 1471-2105

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