2024/06/06/switch-to-bam

[giscus[bot]]

2024/06/06/switch-to-bam

uBAM is a strictly better storage format for your sequencing data, and you should switch to it today.

https://ubinfie.github.io/2024/06/06/switch-to-bam.html

[ammaraziz]

After calling with at least Dorado, ONT sequencing outputs uBAM files.

It's worth noting that I think minknow (with darado) has an option to output .bam files:
nanoporetech/dorado#755

[aretchless]

I checked a few other common tools.

Accepts BAM as input

• bowtie2 (2.5.1)
• fastqc

Does not accept BAM as input (that I can find)

• bwa (0.7)
• blastn
• bbtools
• minimap2
• MEGAHIT
• fastp

[mbhall88]

bwa and minimap2 will accept stdin though, so you can pipe into those from samtools fastq - this is the process recommended by Heng when people ask about other file formats or compression formats