Secret BBMAP helper page - HRGV/Marmics_Metagenomics GitHub Wiki

#How to map to the assembled scaffolds.fasta

bbmap is a powerful and highly flexible read mapper http://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbmap-guide/.

For the upcoming analysis you are not interested in the typical mapping output but in statistics on the coverage on every scaffold, you can get them with scaffstats. We want to be specific with the mapping - we only allow mapping of reads if the read has a minimal identity of 95% using the minid setting. Additionally setting the fast=t switch makes the program work with very fast presets.

bbmap.sh ref=./YOURASSEMBLY/scaffolds.fasta in=YOURTRIMMEDREADS.fq.gz minid=0.95 fast=t covstats=YOURFILE_COV_GC_stats.txt

Done