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Old 09-10-2016, 09:44 PM   #3
Location: Israel

Join Date: Mar 2014
Posts: 26

These are isolate libraries.

When I BLAST short contigs (<200bp) with high coverage (10'sx), these are often parts of ribosomal genes. When I BLAST contigs of length 200-~500bp, where most of low coverage contigs are, these are often pieces of different species in the genus or so isolates not identified to species level.

So the question is then what is "coverage much lower than normal"? Should I stick to a standard cut-off for all genomes? What this cut-off usually is? Or the "auto" mode in SPAdes should be enough?
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