The pattern counting is something I'm especially stoked about. I was actually very surprised to see that this feature isn't more common on grep-like tools (outside of bioinformatics as well).

I've had this problem for years and I end up writing bespoke tools that do some variation of it.

And stay on the look out the next couple weeks (hopefully) for the release of an even bigger project built with binseq!

And if you're interested in building with binseq here is the place to start!

github.com/arcinstitute...

I've also added some nice functionality to bqtools including a very useful colored grep!

github.com/arcinstitute...

Have you tried samply?

The workspace publishing has been such a hassle. So glad to see this out

Sounds great! Would be very interested in that and happy to help build one

bsky.app/profile/noam...

Here was a benchmark I ran a while back comparing twobit and binseq on a single-thread

2bit was built for genomes where there are very long contiguous N-blocks. the overhead for managing these blocks though on fastq-style records (generally very short and non-contiguous Ns) is massive and most of the time unnecessary.

Are you going to have a remote component to this? Would love to watch some of these talks if I can

Ah this is the way that I do it in paraseq! Doesn't work for fastq headers but works well for fasta