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I have a simple/naive thought re reverse-hashing the kmers. We can provide an option to Minhash `reversible = True` to use a reversible hashing function like the Integer Hashing to retrieve back canon…
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Which kmers drive divergence from reference population in windows/features with extreme KLI scores.
Helper script: Given sequence (string or fasta) and Self-kmer pickle file, report observed kmers ra…
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When testing on real fasta files the script takes a long time. This function is relatively easy to run on multiple cores.
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## Expected Behavior
[dataset.zip](https://github.com/user-attachments/files/16023829/dataset.zip)
I have a group of sequences which is properly aligned with almost full length and >95% identity usi…
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Hello Chirag,
Does fastANI compress kmer/minimizer strings by default? I did not see it after checking. I realized that kmer counting from Heng Li's repo (based on kseq.h) (https://github.com/lh3/k…
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Hi! I'm using `sourmash signature kmers` to extract kmers and a fasta from a signature of hashes of interest and the original fasta file.
My command:
```
sourmash sig kmers --signatures --sequ…
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It auto determines the best kmer sizes as 55, 87, and 121. Can I lower the kmer sizes because I get a "too many erroneous kmers" warning?
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Presumably now is the right time to build into Atlas the policy of ignoring kmers in an allele which we know exist elsewhere in the genome
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Hello,
I'm trying to use the STAT tools to build a database from fasta sequences, and then using it to do metagenomics/taxonomic analyses.
So I'm following the tutorial in the build_db_and_run.sh …
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Hi, I found the pangenie-index calculate the unique kmers in the variant flank sequences, so could you please tell me what the unique kmers are used for pangenie genotyping?