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Hello, in my project I would like to just calculate the kmer counts for one side of the reads, read_1.fq.gz, for example.
And then afterwards, I would like to compare kmer.dump across samples, I wou…
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In the documentation it says that ambiguous bases are excluded for the purpose of calculating confidence score.
But I've been getting some slight errors when running kraken2, which led me to try doin…
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Hi All,
I am trying to extract features from a given fasta file (DNA or RNA), using kmer.py script as per the description in the README. While running the code in a juypter notebook it is throwing th…
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spacegraphcats.cdbg.index_cdbg_by_kmer is both slow and memory intensive, sigh.
speed may require more Cythonization or something.
in terms of memory intensitivity, one problem right now is that…
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CC @camilogarciabotero, ref. #297
How would a user go about findings ORFs with BioSequences? To do this, they need to be able to do several fundamental operations that BioSequences currently doesn…
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Hey @lh3, this looks great.
But we do low-coverage (5x) sequencing of many (non-human) individuals - where removing rare kmers is a bad idea. So our ideal approach is to combine all data into a big …
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I have created new class for columns you will find a file called defaultColumn
and I added new functions in kDataframe base class
void addColumn(string columnName, Column*);
template
T g…
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Hi, I found the pangenie-index calculate the unique kmers in the variant flank sequences, so could you please tell me what the unique kmers are used for pangenie genotyping?
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[_3_mytax.txt](https://github.com/xa6xa6/metaOthello/files/1402534/_3_mytax.txt)
I'd like to construct a custom database with a couple million sequences. To start, I decided to try and make a cust…
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I've tried to run kProcessor with kmer size 11 and it threw an error
```
Floating point exception (core dumped)
```
The same happens with kmer sizes 13,15,17
After decreasing the MQF "q" value…