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I am running a file with several Fasta sequences with Jellyfish v. 2.2.1.
I get different results for Kmer counts for 15 5mers. Sometimes there is up to 2fold difference in numbers
some example…
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Hi Marc-André,
I tried katcher and add_pvalue and they work fine, thank you.
However when I try to run `bedtools bamtobed` on the output of add_pvalue, it does not recongnize the value in the PV tag…
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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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`singularity exec ~/software/pangenie/container/pangenie.sif PanGenie-index -v keepA_C_0.5missing_100kbub_phased_deleteN_id_trim_filtered_SVs.vcf -r ZS11.genome.fa -t 24 -o PanGenie`
My vcf sequ…
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Hi I am trying to use the kitsune tool which uses jellyfish to calculate the best/optimal kmer size for counting but when I go to run the command I get this error:
```
Computing Cumulative Relativ…
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Our use of objects instead of strings for graph creation slowed down performance, probably due to the additional allocation.
```
2019-06-19 14:33:34 panther prairiedog[21158] DEBUG Done graphing S…
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Hi
Thanks a lot for this awesome tool!
I am trying to phase an allopentaploid genome which we expect to have 4 subgenomes. Although the clustering works very well, I having trouble to adjust the s…
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Hello there!
I'm interested in using `khmer` to count and filter kmers from transcriptome datasets and then use the raw kmer counts across multiple (~10) samples as the "X" matrix for a classificatio…
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* OS: OS X
* Version: `mccortex=v0.0.3-610-g400c0e3 zlib=1.2.11 htslib=1.8-17-g699ed53 ASSERTS=ON hash=Lookup3 CHECKS=ON k=3..31`
Preparation:
```
$ wget http://ftp.ebi.ac.uk/pub/software/bigsi/…
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The catlas output files are described at a couple places. I found [this page](https://spacegraphcats.github.io/spacegraphcats/01-running-spacegraphcats/) the most comprehensive. However, the descripti…