Table 10

Assembly reconciliation tools performances on human chromosome 14.

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'


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.

Vicedomini et al. BMC Bioinformatics 2013 14(Suppl 7):S6   doi:10.1186/1471-2105-14-S7-S6

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