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krust is ak-mer counter - a bioinformatics 101 tool for counting the frequency of substrings of lengthk within strings of DNA data.krust is written in Rust and run from the command line. It takes a FASTA file of DNA sequences and will output all canonical k-mers (the double helix means each k-mer has areverse complement) and their frequency across all records in the given data.krust is tested for accuracy againstjellyfish.

krust: counts k-mers, writtenin rustUsage: krust<k><path>Arguments:<k>     provides k length, e.g. 5<path>  path to a FASTA file, e.g. /home/lisa/bio/cerevisiae.pan.faOptions:  -h, --help     Printhelp information  -V, --version  Print version information

krust supports eitherrust-bio orneedletail to read FASTA record. Use the--features flag to select.

Runkrust withrust-bio's fasta reader to count5-mers like this:

cargo run --release --features rust-bio -- 5 your/local/path/to/fasta_data.fa

or, searching for21-mers withneedletail as the fasta reader, like this:

cargo run --release --features needletail -- 21 your/local/path/to/fasta_data.fa

krust prints tostdout, writing, on alternate lines:

>114928ATGCC>289495AATCA...