what "Main genome assembly score" in the output file of BBMap mean when evaluating a genome's assembly quality

Question

[Yingzi Zhang]

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

[jean.elbers]

1. What BBTool are you using to get this output? bbstats.sh or statswrapper.sh?
2. Also what version of BBMap is the output from?

[Yingzi Zhang]

I used stats.sh. The version of BBMap is Version 38.31

[Yingzi Zhang]

The command is stats.sh in=genome.fa gchist=scaffold_histogram shist=scaffold_length_histogram extended=t pdl=t score=t > bbmap.log