I have assembly my reads with MEGAHIT to get final contigs. Then I mapping back my contigs with raw reads to get coverage rate with
bbmap/bbwrap.sh ref=megahit/IA_result/final.contigs.fa in=raw_data/IA_1.fq in2=raw_data/IA_2.fq out=IA.sam.gz kfilter=22 subfilter=15 maxindel=80
bbmap/pileup.sh in=IA.sam.gz out=IA_mapping.txt hist=IA_histogram.txt
I got result like this:
Average coverage: 4.25 Percent scaffolds with any coverage: 99.91 Percent of reference bases covered: 98.83
How to interpret the result? Is the result better enough?
Thank you, Nisrina