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COMBINE-lab / cuttlefish

Building the compacted de Bruijn graph efficiently from references or reads.
BSD 3-Clause "New" or "Revised" License
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gzipped input? #11

Closed ctb closed 2 years ago

ctb commented 2 years ago

hi, thanks for releasing 2.0! I successfully installed and ran it on Mac OS X 🎉 (and presumably Linux will just work :).

Our workflows generally produce gzipped FASTQ files after preprocessing. It seems like cuttlefish does not currently support them; thought I'd drop this issue here to check in and let you know that we'd love that support :).

jamshed commented 2 years ago

Hello Titus,

Cuttlefish does support gzipped inputs! Could you please paste here what commands are you trying to use for cuttlefish, and what error messages are you getting?

Thanks!

ctb commented 2 years ago

excellent! I double-checked and (of course) you're right. I think I was trying on a gzipped FASTA file rather than a FQ file at first, and I never went back and checked with a proper FQ file. Thanks!