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Coverage information for contigs assembled by Megahit #168

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Chongli-90 opened this issue Nov 2, 2022 · 0 comments
Open

Coverage information for contigs assembled by Megahit #168

Chongli-90 opened this issue Nov 2, 2022 · 0 comments

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@Chongli-90
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Chongli-90 commented Nov 2, 2022

Greetings!

I am using the shovill - megahit assembler to generate the influenza contigs from the Illumina reads. Unlike the spade, I found all the generated contigs in contigs.fa files from megahit have the same number of coverage (cov) information, which should be the number I put in the input command for --depth. At the same time, I found the cov information in the assembly graph file (contigs.fastg) was different between generated contigs. Were the cov value in contigs.fastg is the coverage value reported by the megahit for the contigs?

For example,
The same contig in contigs.fa file:
截屏2022-11-02 上午12 52 19

in contigs.fastg file:
截屏2022-11-02 上午12 52 02

Does the cov 1956.2868 is the coverage information reported by the assembler?
Thank you so much for your help!

Regards,

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