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Stats Guide
Written by Brian Bushnell
Last updated December 22, 2015
Stats is designed to generate basic assembly statistics such as scaffold count, N50, L50, GC content, gap percent, etc. It can also generate per-sequence GC-content information. The reason for the existence of stats is to replace prior tools that had similar function, but could not scale to large metagenomes; Stats is capable of processing an assembly of practically unbounded size, with sequences of practically unbounded length. And it does this rapidly, in a small amount of memory. Stats can also estimate the memory requirements of BBMap for a given assembly and kmer length.
*Notes*
Memory:
Stats uses 120MB of RAM regardless of the assembly size.
Threads:
Stats is singlethreaded; it does not do garbage-collection or even use independent threads for I/O streams, unlike other BBTools.
*Usage Examples*
To get stats on an assembly:
stats.sh in=contigs.fa
To compare multiple assemblies:
statswrapper.sh in=a.fa,b.fa,c.fa format=6
To print GC and length information per sequence:
stats.sh in=contigs.fa gc=gc.txt gcformat=4
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