sourmash

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`multigather` CSV output uses signature `filename` as basename.

8

In #2321 and https://github.com/sourmash-bio/sourmash/pull/2322 we delve back into multigather... and I remembered how annoying the CSV output is, in that it is output to the signature `filename` for each query....

ctb

add talks about sourmash to docs

9

luiz's talk about how we develop/design/evolve sourmash: https://www.youtube.com/watch?v=0jpnP8NtRfc&feature=youtu.be

ctb

Thinking about further `gather` performance improvements.

3

This is a summarization of remaining issues in #838, which has become unreadable :) ---- from @luizirber in https://github.com/dib-lab/sourmash/issues/838#issuecomment-573856948: I'll dump here some other pointers to `gather` improvements, and they...

ctb

other makeshift strategies for large scale database search - the "greyhound" issue

16

I'm on day 3 of a gather of the Hu S1 dataset against all genbank (500k+ genomes), and chatting with @taylorreiter about the find-the-unassigned script that @luizirber wrote, https://github.com/taylorreiter/cosmo-kmers/blob/master/scripts/unassigned.py it...

ctb

some more hot take ideas on making search and gather faster, for interactivity purposes

2

while I'm thinking about it... it would be nice to move towards genuinely interactive search, gather,and MAGsearch. greyhound #1226 and greyhound.sourmash.bio/ is super cool, of course, but it's "only" searching...

ctb

optimizing gather on large databases - some thoughts in re benchmarking

2

from [benchmarking on 1.2m signature genbank](https://github.com/dib-lab/2020-paper-sourmash-gather/issues/47), even fairly simple environmental metagenomes such as SRR1976948 are matching to lots of redundancy. we're looking at ways to deal with this at a...

ctb

Luiz's talk on August 30th, 2022 at the annual JGI User Meeting: https://luizirber.org/talks/2022-08-30-JGI/slides.html

ctb

Bump serde_json from 1.0.85 to 1.0.86

1

Bumps [serde_json](https://github.com/serde-rs/json) from 1.0.85 to 1.0.86. Release notes Sourced from serde_json's releases. v1.0.86 Support arbitrary_precision feature even in no-std mode (#928, thanks @​kvinwang) Commits 4217e8e Release 1.0.86 99d6164 Reorganize number.rs...

dependabot[bot]

keep strand

4

Hi, according to the manual at the moment, the reverse complement and in case of is_protein=True all 6 possible open reading frames are considered. Is there an option to keep...

kullrich

I just ran gather on some genomes (attaching a snippet of results below). These are all single genomes. ``` overlap p_query p_match avg_abund --------- ------- ------- --------- 5.3 Mbp 44.2%...

taylorreiter