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Parsoa / SVDSS

Improved structural variant discovery in accurate long reads using sample-specific strings (SFS)
MIT License
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Question on Input Support for FASTA Input for SFS Search #28

Open LeoHongboWANG opened 1 year ago

LeoHongboWANG commented 1 year ago

Hello,

Thank you for developing this tool. I'm using SVDSS search to extract SFS from two assembled contig genomes. The documentation mentions support for FASTA Extract SFS, Extract SFS from BAM/FASTQ/FASTA files: but the command seems to accept only BAM or FASTQ:

SVDSS search --index /path/to/index --fastq/--bam /path/to/input --workdir /output/directory

Could SVDSS search accept FASTA files? If so, how should I modify the command?

Many thanks, Hongbo

ldenti commented 1 year ago

Hi, which version are you using?

In v1.0.5 (bioconda) you can pass the FASTA file to the --fastq argument (I know this is not intuitive and should be improved..).

Just a note: searching from FASTA/Q is way slower than searching from BAM (but this holds for reads.. maybe it will be faster for contigs).

Best, Luca