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Cram support

Open jjfarrell opened this issue 5 years ago • 2 comments

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

jjfarrell avatar Nov 03 '19 13:11 jjfarrell

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.

marekkokot avatar Nov 04 '19 09:11 marekkokot

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.

jjfarrell avatar Nov 07 '19 15:11 jjfarrell