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Hello,
I'd like a list of kmers from a cyclic graph, but `vg kmers -k 20` doesn't seem to be outputting those that follow the edge connecting the tail node to the head node.
![screenshot from 201…
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In `skbio.distance` you've got experimental function `kmer_distance`, which is basically the `1 - J(s1, s2)`, where `J` is the Jaccard index function, and `s1`, `s2` – two sets of kmers. The Jaccard …
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Use shorter kmers for initial seeds
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Hi, @EricR86 @mehrankr
Thanks for providing an excellent program for calculating genome mappability. I'd like to inquire about a few questions I've had while running umap here.
1. I'm using the…
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Hi @akcorut ,
I am running kGWASflow on a VM hosted on our server with 7TB Hard Disk and 180 G RAM.
I got this message:
[Thu Oct 12 01:53:07 2023]
Job 2972: Running k-mers based GWAS on /mnt/Data-…
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Would it be possible to add a feature to run meryl-lookup exclude/include on a BAM instead of a fasta and output BAM? This would be very useful for filtering reads from PacBio or ONT data in their or…
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Re #7 : Consider adding read-level scores and thresholds. Possible scores:
- `kraken-filter` score: `taxon_kmers / unambiguous_kmers`
- [Andersen](https://bmcmicrobiol.biomedcentral.com/articles/…
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Hello,
I am currently running into an issue when assembling contigs for k=21. This is for an assembly of 172 GB of data using 900GB of memory and 10 CPUs. I have pasted the log output below. I co…
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Currently, one can't make 0-length kmers:
```
julia> DNAKmer(dna"")
ERROR: ArgumentError: Bad kmer parameterisation. K must be greater than 0.
Stacktrace:
[1] checkmer(#unused#::Type{DNAKmer{0…