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Dear KrakenUniq team,
I have a theoretical question - I was wondering if you could suggest something here. I am using KrakenUniq to classify bacterial reads from RNA-seq experiments. The database …
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The version 3.2.0 update says that the "possibility to store only k-mers in the database (no counters)" was implemented; however, I don't see any documentation on how to do this. I m building some ve…
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I wanted to use `Maast`'s sck-mer database construction command `db` on a set of VCF, MSA Fasta, and reference.fna (Klebsiella _pneumoniae subsp. pneumoniae_ reference genome KPNIH1) files which are …
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Hello!
I run:
**reckoner -genome 4500000000 -prefix ${p} -threads 128 -kmcmemory 900 -longkmer -verbose -reuse ${r1} ${r2}** …
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RSAT `position-analysis` detects k-mers that present any type of positional heterogeneity by running, for each k-mer, a chi-squared homogeneity test on its profile of counts per positional windows com…
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I can load my fasta and run the indexing function fine, but it simply produces nothing. The outpout looks like below in my terminal:
[build] loading fasta file Homo_sapiens.GRCh38.cdna.all.fa
[bui…
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Why not allow gapped k-mers exists to search the best LCA?
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This text:
> This work is made possible by the open sharing of genetic data by research groups from all over the world. We gratefully acknowledge their contributions.
is added to any dataset on …
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code in #40 could benefit from making `SeqToHashes` less opaque over in sourmash.
Some ideas:
* simple and lightweight: provide access to `kmer_index` per https://github.com/oxli-bio/oxli/pull/4…
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The description of the output format of the headers in the contig output fasta file is intelligible:
See screenshot:
![image](https://github.com/user-attachments/assets/d8ad4ba5-4c5c-4939-8f2f-4…