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jts / sga

de novo sequence assembler using string graphs
http://genome.cshlp.org/content/22/3/549
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add kmer-count command #74

Closed pradosj closed 10 years ago

pradosj commented 10 years ago

This is an implementation of a kmer-count command in SGA, inspired by the implementation of method extract in BWTTraverse.cpp. This new command is able to list the kmers of a BWT, and count the number of time they appears into another BWT. This can for example be useful to perform a variant calling, by listing the kmers from a readSet that are missing into another readSet.

The command is not parallelized, and I do not plane to implement this feature for the moment.

jts commented 10 years ago

Thanks for this. I'm traveling at the moment but will merge when I get home.

jts commented 10 years ago

Looks great, thanks for adding this.