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ibest / ARC

Assembly by Reduced Complexity (ARC)
Apache License 2.0
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Track expected coverage #7

Open samhunter opened 11 years ago

samhunter commented 11 years ago

Maintain information about the length of contigs and calculated expected coverage, using this, add a -e switch to Newbler (Spades doesn't seem to support expected coverage, but research this further).

asl commented 11 years ago

Indeed, SPAdes does not support this option, because it does not require it (Newbler is OLC assembler and thus can blow up with high coverage data).

One can obtain a lot of useful information from spades.log though. For example, the expected coverage deduced from the k-mer coverage histogram, estimated genome size and final coverage of the graph.