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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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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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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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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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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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Hi , I followed the guide strictly, but I get this error, I don't know what's causing it? Thank you!
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Why not allow gapped k-mers exists to search the best LCA?
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For canonical k mers, which ATCG combination is dropped?
For example, AAA, TTT, the kmc will dump all TTT counting to AAA or vice versa?
What's the rule? Thanks!
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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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Hi,
I was wondering if it is possible to include an argument in kmer-db that allows the inclusion of non-canonical k-mers in the construction and querying of databases. Thus far I have been using a m…