sourmash
sourmash copied to clipboard
sourmash-bio
Quickly search, compare, and analyze genomic and metagenomic data sets.
how to run the tests right: https://github.com/sourmash-bio/sourmash/pull/3138#issuecomment-2104746508
based on some of the results for the new long-read benchmarking paper Portik et al. ([link](https://www.biorxiv.org/content/10.1101/2022.01.31.478527v1) - not yet updated), @bluegenes and I were discussing ways to decrease the false...
Hi again! Just thinking about the RefSeq versus GenBank question for analysis of a metagenome (containment). Aware that Sourmash may struggle with similar genomes (ie strains) due to a smaller...
Hi @ctb the sourmash author, Currently we are working on using your tool to find the representative MAGs within a customed data set assembled from several deeply sequenced stool shotgun...
https://github.com/sourmash-bio/sourmash/issues/3191 was partly caused by my failure to properly use the context manager for saving signatures. A patch fix and test were added in https://github.com/sourmash-bio/sourmash/pull/3214, but this should really be...
Extracting from issues reported in https://github.com/sourmash-bio/sourmash/issues/3191 and https://github.com/sourmash-bio/sourmash/issues/3190 - we get this error on empty zip files: ``` sourmash.exceptions.Panic: sourmash panicked: thread 'unnamed' panicked with 'called `Result::unwrap()` on an `Err`...
the betterplot plugin (#3178 and https://github.com/sourmash-bio/sourmash_plugin_betterplot/) provides some nice additional visualization capabilities to sourmash. We should advertise those on the main sourmash docs, I think.
calc-hash-presence.py from [pangenome-hash-cor](https://github.com/ctb/2024-pangenome-hash-corr), does not yet allow me to compare protein sketches instead of nucleotide sketches. I'd like to compare protein-pangenomes instead of nucleotide ones Trying in `/group/ctbrowngrp2/scratch/annie/2023-swine-sra/sourmash/pangenomics/test_virpan` ``` python...
this might be of use to people looking to grok genome overlaps etc. [notebook permalink](https://github.com/dib-lab/genome-grist/blob/051a96210958afcf7f1d61ce11537796339dc64e/hash-upsetr-example.ipynb) [notebook latest, but link may break ;)](https://github.com/dib-lab/genome-grist/blob/latest/hash-upsetr-example.ipynb)
Pyupset (python) and UpsetR (R) generate nice plots with interactions between sets but pyupset does not print the unique values/groups or the intersection between these sets. @halexand and I can...
Metadata
Owner
Metadata
Quickly search, compare, and analyze genomic and metagenomic data sets.