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I built the ert branch of bwa-mem2 arch=avx12. I get a failure with segmentation fault after from 20 seconds to 1.8 seconds run time. i did not have a problem with the build. I made an index with no p…
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Hi @object022,
I was reading the miniception paper to see if this could be used to improve the density of the minimizers used by [SSHash](https://academic.oup.com/bioinformatics/article/38/Suppleme…
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Hi fbreitwieser ,The web site https://fbreitwieser.shinyapps.io/pavian/ can not support krakenuniq --report-file .Or i missed something. The formats are as follows.
% reads taxReads kmers dup cov t…
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To interpret the learned codes it would help to have the following visualizations:
1. distance matrix clustering for all TFs. Do probes from like families cluster together?
2. Visualizatio…
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# spacegraphcats read indexing
with sgc, we need to be able to go from k-mer to cDBG unitig to read. How is this implemented?
First, we put all of the reads in a BGZF file, which is a gzipped fi…
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At the moment kevlar is painfully slow. We've been philosophizing for a while now whether this was more likely due to the poor cache locality of khmer's Count-Min Sketch implementation or to slow Fast…
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Hi there, I've been applying Plasflow to MAGs from waste water treatment samples, and it seems to be working really well! My question is more theoretical than technical - given that many of our assemb…
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Hello,
I'm running this workflow:
```golang
param (
// S3 path to 10x folder
tenx string
// Full s3 file location to put the sourmash signature
output string
//…
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If ANVIO can pass in the contig lengths then we can filter and only cluster with say contigs > 1000bp. The rest we can still assign to clusters based on responsibilities.
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Write shell scripts that do the following
- [x] Filter 1kg vcf files based on required regions/params
- [x] Intersect two populations (just an example script might be a good start - add this to priv…