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https://github.com/IEDB/PEPMatch/blob/70d4ba9c7adb6d3dd5e20dfa55961f3299d26a7d/pepmatch/preprocessor.py#L186C1-L189C78
Dear Developer(s),
PepMatch is an incredibly useful and well-written tool—t…
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Needs to be documented. Especially because the edge list is now totally sparse.
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I want to generate a db of all kmers and their counts for a reference genome using `meryl count`, then for thousands of small (~1-5 kbp) sequences I want to extract all kmers and find their counts in …
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Dear SqueezeMeta developers,
Recently I requested the SqueezeMeta installation to the Admins of the Supercomputing center we use, but when I got ready to use the SM tool two errors appeared after…
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Hi
I am running KmerDedup on my highly duplicated assembly (created using hifiasm) as the many sample were pooled together (one organism). KmerDedup has successfully generated the shell script. Step0…
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Hello all,
In software docs, the 5 columns of output result file is a space-delimited list indicating the LCA mapping of each k-mer in the sequence(s). For example, "562:13 561:4 A:31 0:1 562:3" wo…
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Hi,
We try to list all possible kmers from a pair of fastq files using:
```
kmc \
-k31 -m128 -ci1 -cs4294967295 -cx1e13 -t36 \
-jOutput.json \
@files.lst \
test.kmer.output \
`pwd`/kmc…
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Hi, @agudys
When I run kmer-db, I always came across the issue of 'out-of-memory', even testing with very small input fasta or the example fa in your 'data' directory. My command is: `kmer-db buil…
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Hi,
Could you help me to understand how QueryContainmentAni and MatchContainmentAni are calculated?
Given the use of exact kmer matches, I would assume that the ANI between a query kmer and a re…
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Dear developers:
openDBA has many applications, which are very interesting. Nanopore provides a kmer model for generating standard nanopore signals. By providing a sequence based on this kmer model, …