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Following up on a discussion I had with @nickp60 earlier on whether or not we should retune the `bbduk` parameters during trimming (given that we have some reads that look like adapter/empty sequence …
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Hi @mourisl,
It was exciting to meet you at CSHL and I appreciate that you took some time to implement the feature we discussed.
I gave it a try this morning, and saving the trusted k-mers file …
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To support finding long k-mers, I tried re-installing in the build folder following instructions:
```
rm -Rf CMake* && cmake -DKSIZE_LIST="32 64 92" .. && make
```
where I chose multiples of 32,…
b2jia updated
3 years ago
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Hello,
As there is nothing mentioned in the manual or other issues, can you please share with me your experiences when running kraken2 on ONT reads.
What is the best kmer-length, the minimizer len…
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I've been trying to get metalign up and running for a metagenomics project I'm working on. I originally realized when I cloned the github repository, the db_info.txt file was not present and was givin…
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Dear developers of this great assembler,
I have a question concerning a weird k-mers histogram with 3 peaks for a definitely diploid fish genome. Please find the attached k-mers histogram as output…
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When using 30X hifi data, 0.16.1-r375 with default parameter produce a larger assembly fasta(the Genome size is estimated to be 2.2G, assembly result is 3.0G).Compared with the kmer distribution of an…
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Hi! Thanks for the great tool! I was wondering if one could get the genomic location of subgenome-specific TE or TE k-mer. My idea is to take a look at coding regions that are upstream and downstream …
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I am trying to run a `foldseek easy-search` job with the UniProt database built from `foldseek databases Alphafold/UniProt`. With two different attempts on different machines (with up to 256GB memory)…
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## Expected Behavior
Summary: Running linclust or clust with a very big database leads to a heavy slowdown in the rescorediagonal part. Expected the job to continue much faster. It releases a warning…