what "Main genome assembly score" in the output file of BBMap mean when evaluating a genome's assembly quality
Dear all,
I used BBmap to evaluate two genomes' assembly quality. The analysis output like this:
>genome Contig_N50 Scaffold_N50 Total_Len(bp) Gap_Len(bp) Gap_Ratio(%) Main genome assembly score
>A 41891233 138966237 2501912388 2472047704 1.19 49.937
>B 25617 5475012 2636501961 2580997266 2.11 49.563
I found nearly all the parameters showed that A had an obviously better assembly quality than B except the parameter 'Main genome assembly score', which was nearly the same of both A and B. Do anybody know how 'Main genome assembly score' is calculated? I looked through the BBmap website as well as its technical details but I didn't find the answer. I didn't even find the entire phrase in neither of the two documents. Till now the phrase only showed up in the BBmap output report.
Thanks for any kind of help in advance.
Best Regards,
Yingzi
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Yingzi Zhang
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BBToolare you using to get this output?bbstats.shorstatswrapper.sh?I used stats.sh. The version of BBMap is Version 38.31
The command is
stats.sh in=genome.fa gchist=scaffold_histogram shist=scaffold_length_histogram extended=t pdl=t score=t > bbmap.log