What are the minimal contig length and kmer coverage below which I should drop some contigs in viral metagenomics study after assembly with Spades?
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3 months ago
bioAddict • 0

Hi Everyone,

I'm performing a virus metagenomics on RNAseq data to characterize the virome of Anopheles gambiae.

After the assembly with SPAdes, I obtained contigs, which measure between 100 pb to 20kb, with variable coverages. What I'm stuck on is below what threshold I can drop some contigs by kmer coverage and contig length.

Please help me.

Kmer Length Contigs coverage Metagenomics • 177 views
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