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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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Would you mind providing a more detail on assembly ? #31

Open deyuanyang opened 1 year ago

deyuanyang commented 1 year ago

Hi,

It's a perfect soft. When I used it to assemble my data, I could not understand the --read parameter, if I have data like R1_fq.gz, and R2_fq.gz， how to use it？ It can use like Spades. -1, -2, -U for input data?

Best wishes, Deyuan

deyuanyang commented 1 year ago

image

jamshed commented 1 year ago

Hi @deyuanyang:

Thank you for using cuttlefish! I see that you're using FASTQ inputs---in that case, you need to pass the --read argument. Besides, I also see that you're using the -f 1 argument, which specifies a specific output format among a few ones. When working with read sets, cuttlefish can only output the assembled maximal unitigs (i.e. contigs) for now, and so the -f option is not applicable.

I think for your example datasets mentioned above, you can use the following command:

cuttlefish build --seq <file-1> --seq <file-2> -k 33 -o <output-file> -t 8

Let me know if that solves the problem(s). Regards!