search

lbcb-sci / raven

De novo genome assembler for long uncorrected reads
MIT License
202 stars 21 forks source link

How could we get the gfa assemble result #80

Closed ld9866 closed 6 months ago

ld9866 commented 6 months ago

Dear developer: We are assembling the genome using raven, but we found that we are having a hard time getting the file in gfa format and there is no such example in the sample file, can you help me? The example coud for fasta: （works well） raven --threads 100 sample.fastq.gz > sample.raven.contigs.fasta but what we want is to get the gfa assemble result ,how could we solve this?

FilipTomas commented 6 months ago

Hi, To output a gfa file, use the -F or --graphical-fragment-assembly option. Both options perform the same functionality, with the former being a shorter alternative to write. E.g. raven --threads 100 -F sample.raven.gfa sample.fastq.gz > sample.raven.contigs.fasta Hope this answers your question.

ld9866 commented 6 months ago

Thank you! we have done this with your help!