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will-rowe
Histosketching Using Little Kmers
Dear Will, With the newest go version 1.16, I have the following error: (base) [jianshu@c391 fasta]$ hulk sketch --fasta -f S_Baltica_OS675.fna -o ./S_Baltica_OS675.hulk.sketch 2021/12/26 18:24:00 this is hulk (version 1.0.0)...
Dear author, First of all, I would like to thank you for providing this novel and interesting analysis tools, however, I do have some questions. 1. Paired-ended fastq data I...
dear will-rowe, HULK is concerned about the k-mer frequency as described in your paper. I find that a minimizer hash value cannot be added into the minimizerSketch when it is...
At the moment, the minimizer package collects minimizers but doesn't retain minimizer ordering from the sequence they were derived. This is because I am using a set implementation based on...
The minimizer algorithm is fairly simple at the moment. If using HULK with long reads, it is probably a good idea to compress the homopolymer runs when collecting minimizers.
There are a lot of conversion between ints (uint64/32/8 and ints) etc. This is unnecessary and makes the code harder to follow. I'll work on reducing these
I need to massage the output from "smash" to create a distance matrix in the same form as that from Mash so I can reuse downstream visualization code. Right now,...
