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synopsis: When running FastK with -k set 32 or less, I'm seeing segfaults.
Specifically, I've seen this with one particular input file (the blue whale assembly) and k in {20,26,31,32}.
Details:
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We classified metagenomic reads using a custom database.
This is the Kraken2 classification for an example paired read (from the .krak file)
taxid 2161 83|86 0:42 2161:5 0:2 |:| 0:1 2161:1 0:3 2…
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See https://github.com/dib-lab/kevlar/issues/31.
Accumulate hashed k-mers in some kind of buffer1. The first time the buffer reaches a user-specified size, go through each band one-by-one, create a…
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I have put a small example on [this gist].(https://gist.github.com/winni2k/64efa2e354a70a72d8a70a5ac373cc49)
When I run `run.sh`, I get the following output:
```bash
0 reads pseudoalign
[build…
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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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I am trying to build a kmer db using the k-mer output from KMC but I keep getting an error.
This is the command I am running:
```
./kmer-db build -from-kmers ./KMC.list ./output/KMC_out.db
```
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I have an application where I need to count pairs of k-mers separated by a fixed distance. This is almost identical to K-mer counting where K=2k, the "only" change should be in the scanning step where…
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David Koslicki convinced me this was a good idea.
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https://hackmd.io/9ORFRJGaTOiOdEAY-Aih2A?view
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# open lab / Sat + Monday , Jul 20 & 22, 2024 / STAMPS 2024
Suggestion for open lab:
* run the commands below on the "canned" data;
* diagr…
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## Feature request
### Tool(s) or class(es) involved
_StructuralVariationDiscoveryPipelineSpark, XGBoostEvidenceFilter.java_
### Description
Currently there are two unresolved large structural…