what are the various MAGsearch-related repos? - Githubissues

sourmash-bio / sourmash

Quickly search, compare, and analyze genomic and metagenomic data sets.

http://sourmash.readthedocs.io/en/latest/

Other

472 stars 80 forks source link

what are the various MAGsearch-related repos? #2332

Open ctb opened 2 years ago

ctb commented 2 years ago

these have accumulated over time with recent wild proliferation...

which ones am I missing? 😭

actual core repos

https://github.com/sourmash-bio/sra_search - actual searcher code in Rust
https://github.com/sourmash-bio/wort - automatically download and process SRA datasets
https://github.com/dib-lab/2022-paper-magsearch-software/ - manubot paper repo for draft tech/software paper
https://github.com/sourmash-bio/mastiff/tree/latest/crates/server - 🦮 repo for realtime search

example and demo repos

https://github.com/luizirber/2020-07-22-mag-search/ - luiz repo containing good stuff
https://github.com/sourmash-bio/2022-search-sra-with-mastiff/ - repo for titus blog post/binder notebook

repos of convenience

https://github.com/ctb/magsearch/ - the repo titus actually uses to run magsearch; contains tests etc for magsearch that he started writing before he resolved to just !#%!%# take on learning rust
https://github.com/luizirber/2022-06-26-rocksdb-eval/blob/latest/src/main.rs - mastiff indexing repo. "Ideally the indexing one disappears with the mastiff PR merged in sourmash. - luiz"

ctb commented 2 years ago

misc useful info: how to update runinfo https://github.com/ctb/magsearch/issues/8