(Relatively) Easily get coverage for velvet assemblies
02 Jul 2011 \\ bioinformatics
You can get kmer coverage from contigs assembled by velvet by parsing the kmer value from the output fasta header, but sometimes I want "actual" coverage for contigs or coverage across a specific subset of contigs.
Here is a way to do this relatively painlessly (requires that you first download and build the amos tools).