Question on Input Support for FASTA Input for SFS Search

[LeoHongboWANG]

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]

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