Interpret coverage from mapping back de-novo assembly
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17 months ago
nisrinalulu ▴ 10

Dear all,

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

and

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

assembly metagenomic next-gen • 273 views
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