Hi, I would like to know to average coverage of my assemblies (gotten by spades). I ran bbmap to mapping my reads (the same ones I used to make the assembly) to the assembly. But I am not really sure that is the way and the answers on the different forums didn't completely help.
bbmap.sh in=./trimmed/NM167_S34_R1.fastq in2=./trimmed/NM167_S34_R2.fastq ref=./assembly/NM167_S34.fasta covstats=covstats.txt
I got output like this:
#ID Avg_fold Length Ref_GC Covered_percent Covered_bases Plus_reads Minus_reads Read_GC Median_fold Std_Dev NODE_1_length_79421_cov_85.482448 261.1709 79421 0.5185 100.0000 79421 60378 60230 0.5259 253 111.34 ....
I will really appreciate your help!