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So after trying to write some code interfacing `kmers` with some k-mers parsed using `needletail`, I realized we are storing the k-mers in the opposite order. In `kmers` the leftmost nucleotide is st…
rob-p updated
2 years ago
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Hello,
I'm using Nanocompore to compare between a modified sample and an IVT sample.
I've already done the nanopolish collapse step and I got this in the log file (for the IVT sample, the modified…
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I would like to ask how Trust4 can directly analyze paired-end .fastq format data from the 10X Genomics platform for single-cell analysis, instead of analyzing BAM format data. Can you provide support…
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Hi guys,
I downloaded the refseq database and I wanted to create its Karp index but it failed.
The following message was printed :
"**_Counting kmers ... terminate called after throwing an i…
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Hi again!
Just thinking about the RefSeq versus GenBank question for analysis of a metagenome (containment). Aware that Sourmash may struggle with similar genomes (ie strains) due to a smaller numb…
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Thank you for developing this pipeline.
I've noticed that for my allotetraploid species, while -k 15, -k 14 works fine, once I try -k 13 or -k 12, there are a lot of broken pipeline issues. A lot …
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Maybe both sequences can be made into a dictionary of kmers. FIRST CHECK IF THIS WILL SPEED UP CODE (it will reduce memory)
Needs:
Function
Update to work with the function
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Hi, thanks for this useful software,
I was using this tool, and currently wondering if it is possible to generate a affinity table for each enriched k-mer in a library. I found one tool in bioconduc…
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Hi Hongzhe,
I tried to run your tool on a standard reference human genome data set (GRch37).
This is the command I used to run indexing process:
`./deBGA index -k 27 GRch37.fa `
First of a…
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Large kmers help to sort out strain variants thus using a k of 51 with sourmash or kraken may be the best way to go.
### Expected behavior
### Actual behavior
### Steps to reproduce the …