Can kmtricks exploit an alternative to Jellyfish2?

[zhangwenda0518]

Hello teacher, I am running a large dataset, and when I was looking up literature, I saw that https://github.com/tlemane/kmtricks tool could use kmtricks to replace Jellyfish2 to speed up the operation and reduce memory consumption

ref：Téo Lemane, Paul Medvedev, Rayan Chikhi, Pierre Peterlongo, kmtricks: efficient and flexible construction of Bloom filters for large sequencing data collections, Bioinformatics Advances, Volume 2, Issue 1, 2022, vbac029, https://doi.org/10.1093/bioadv/vbac029

[mourisl]

It's possible. The main program of rcorrector (not the wrapper of run_rcorrector.pl) uses the option "-c" that takes a fasta-like file for canonical kmers' count as:

>count1
kmer1
>count2
kmer2

If the methd can dump the kmer count in this fashion, you can directly run "rcorrector".

Hope this helps.