Bam file as input ?

[BenjaminGuinet]

Hello, as I have a lot of bam files, and to avoid taking too much space and extracting the reads, I wanted to know if Metabuli could handle a command like this:

samtools fastq --threads 16 Myfile.bam | seqtk seq -A - | metabuli classify --seq-mode 1 RefSeq_metabuli_db Metabuli_classify_short_reads Classify_short_reads --min-score 0.15 --min-sp-score 0.5

I tried this but it does not seem to work.

Any idea about another way to do this?

Thanks a lot.

[jaebeom-kim]

Sorry for the delayed answer. Currently, Metabuli doesn't support BAM input files and standard input. I think your command is not working since Metabuli doesn't take standard input as query sequences. Let me try two things.

• Supporting BAM files
• Supporting standard inputs.

Thanks a lot!