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I'd like to understand why kmc gives an empty output for several genomes.
The genome I downloaded and tried to analyze was [https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/067/135/GCF_001067135.1_…
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$P$(observe k events) =
Here the parameter $\lambda = \frac{M}{S}$ is the expected number of hashes
for $M$ k-mers at a scaled of $S$.
$P$(k hashes for M k-mers with scaled S) = ${\exp(-M /…
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Hi,
I tried assembling the mitogenome of my insect species using MitoZ. The final assembly is not circular, with a size of 15,442 kb. Additionally, the following genes are missing:
l-rRNA
tRNA-…
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one of the main challenges right now is estimating memory requirements for cDBG/k-mer indexing stage.
I think we could figure out how much memory to provide to sgc if we knew how many distinct k-me…
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Suggestion from @drtamermansour: in a single pass, write count tables to N files (one for each band) in a single pass. Then running `kevlar find` in N bands would not require N passes over the entire …
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Related to the https://github.com/marbl/ModDotPlot/issues/29 I thought to investigate by using test sequences.
I take a sequence from arabidopsis chr1 and copy paste a sequence 3 times,
```
%%…
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General Coding Tips:
1. Avoid the use of hard-coded numbers. It’s best to define your variables under a reasonable name and use them within the rest of your code so that we can understand where the…
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Hi @yoshihikosuzuki ,
I am using ClassPro like this:
`$ ClassPro -v -T16 -NResults/13_profile_reads/Profile_17_mers -r7000 Results/11_preprocess_fastq/My_file.fastq.gz`
And get this output:
```
…
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I am struggling to understand the useful looking `-F` option, which allows one to pass a fasta file from which k-mers are extracted and used as reads. I suspect I have misunderstood the manual:
```…
bede updated
10 months ago
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Hi,
when I try to run vargeno on the same data linked in my previous issue (https://github.com/medvedevgroup/vargeno/issues/2), it crashes during the geno step.
This is the output of `vargeno inde…