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refresh-bio / KMC

Fast and frugal disk based k-mer counter
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Cram support #141

Open jjfarrell opened 4 years ago

jjfarrell commented 4 years ago

Does KMC support the reading of crams? All my newest sequencing data is in cram format.

marekkokot commented 4 years ago

Hi, unfortunately, currently, KMC does not support CRAM input files. We will consider adding support for cram files, but I am afraid it may take some time.

jjfarrell commented 4 years ago

Could a cram be streamed with samtools to KMC standard input as a short term workaround? This would help minimize the storage requirements and increase the throughput.