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kmtricks is a modular tool suite for counting kmers, and constructing Bloom filters or kmer matrices, for large collections of sequencing data.

kmtricks is optimized for the analysis of multiple FASTA/FASTQ files (gzipped or not).

Its features:

• Fast k-mer matrix construction
• Fast Bloom filters construction
• Rescues low-abundance k-mers when they are seen in multiple samples

Note: when counting kmers from a single file, kmtricks works but is slightly slower than a traditional k-mer counter (e.g. KMC). It is really optimized for counting and merging count information across multiple samples, which traditional kmer counters cannot do.

Reporting an issue

If you encounter a problem, please open an issue with a description of your run and the return of kmtricks infos. If you encounter a critical error like a segmentation fault, kmtricks automatically dumps a file kmtricks_backtrace.log in your current directory. This file is somewhat illegible in release mode. If you can, compile kmtricks in debug mode (see installation), launch it again and join the content of this file. If you cannot directly compile kmtricks on your system, the conda package provides kmtricks-debug binary.

Contacts

Téo Lemane: teo[dot]lemane[at]inria[dot]fr
Rayan Chikhi: rayan[dot]chikhi[at]pasteur[dot]fr
Pierre Peterlongo: pierre[dot]peterlongo[at]inria[dot]fr