What are the minimal contig length and kmer coverage below which I should drop some contigs in viral metagenomics study after assembly with Spades?
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.
• 936 views
•
link
written
by
bioAddict •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Too many contigs in Spades output
written by waqaskhokhar999
-
Extremely high variance of coverage for metagenomic sample (variance-to-mean ratio ~2.5)
written by k-tarasov •
-
Assembly finished but output contig file is empty
written by tchow5 •
-
Neophyte in WGS. Advise for an hypothetical pipeline.
written by lugonauta •
-
Criteria for filtering contigs after spades assembly
written by fhsantanna
-
Metavelvet fails at Scaffolding stage
written by jamesT •
