Mash
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marbl
Fast genome and metagenome distance estimation using MinHash
Hi all, first some background: it seems like [sourmash](https://github.com/dib-lab/sourmash) is going to be a thing; I'm building it into a metagenomics data exploration tool, and it's already integrated into [https://github.com/dib-lab/khmer/](khmer)...
I am trying to find similar sequences of a given query sequence. I am assuming all sequences are of same length and I have to find the similar ones from...
JSON schema
A first pass of the JSON schema is in the Mash repo: https://github.com/marbl/Mash/blob/master/src/mash/schema.json For now, I put k-mers as a separate array parallel to hashes rather than an array of...
There are 3 `mash sketch` use-cases but only 2 are currently possible. 1. `mash sketch a b c` will create a single sketch of all 3 (`a.msh` by default) 2....
Mash output (and sketches) currently represent the input file names as given, with paths: `/path/to/input.fasta` It would probably be better to strip them to basenames: `input.fasta` We would just have...
Dear Developers and other users:\ I'm now trying to use the `mash screen` to detect potential contaminants within my NGS data. Now I'm following a tutorial offered by the developers:...
When sketching a large number files, the mappings left in place from Sketch::initParametersFromCapnp will overrun the allowed number of mappings and cause mmap to fail. This patch removes the mapping.
If one goes to the github repo, one has no idea what MASH actually does from the README
Hello Team, When I run this line of code: "mash-Linux64-v2.3/mash sketch -o bacteria_reference bacteria_fa/*.fna", I am prompted with 'mash-Linux64-v2.3/mash: Argument list too long'. Is there a good solution? Thanks, Dr....
Compiling mash fails on Red Hat Enterprise Linux 8.6 (Ootpa) because of a missing include in `robin_hood.h`. See https://github.com/martinus/robin-hood-hashing/issues/125 for the fix upstream in robin-hood-hashing, and #167 in this repository....
