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...there's no reason we need to stick with k-mer-based signatures alone. what would this look like?
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when installed from conda, the sourmash shared library is installed in the environment `lib` directory as `libsourmash.so`; however, from PyPI, the library is nested under site-packages as `_lowlevel_…
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try to tick as many boxes as possible from http://python.apichecklist.com/, per https://github.com/dib-lab/sourmash/issues/174#issuecomment-306005416
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https://github.com/ngs-docs/2017-ucsc-metagenomics/pull/3
[direct link to notebook](https://github.com/ngs-docs/2017-ucsc-metagenomics/blob/clustering/files/sourmash_tetramer-cluster-extract.ipynb)
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I have a simple/naive thought re reverse-hashing the kmers. We can provide an option to Minhash `reversible = True` to use a reversible hashing function like the Integer Hashing to retrieve back canon…
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While working on https://github.com/sourmash-bio/sourmash/pull/1808, I started thinking about the `find` protocol implementation for several Index types (`SBT`, `LCA_Database`, and the maybe-soon `Sql…
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Had an error shared with me (🎉):
```
Error in `dplyr::select()`:
! Can't subset columns that don't exist
x Column `n_unique_kmers` doesn't exist.
Run `rlang::last_error()` to see where the erro…
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search at https://www.ncbi.nlm.nih.gov/sra/ for "METAGENOMIC"[Source] NOT amplicon[All Fields]
direct link courtesy of luiz:
https://www.ncbi.nlm.nih.gov/sra/?term=%22METAGENOMIC%22%5BSource%5D…
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I use `-k` quite a bit to select a subset of tests, as well as specific files -
e.g.
```
py.test tests/test_sourmash.py -k sbt
```
would run all of the tests from `test_sourmash.py` with `sbt` …
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Hello,
I came to know that sourmash search databases for IMG genomes have been prepared recently.
(http://ivory.idyll.org/blog/2017-taxonomic-disagreements-in-tara-mags.html)
Are these sourmash…