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K-meriser

Takes an input reference genome, refernce index, k, and number of threads and generates for each chromosome a tsv file containing the unique overlapping k-mers in it, their position relative to the chromsome, their position relative to the genome start, and their number of ocurrences.

TODO: add a step in the end to merge the results from the different chromosomes.

Prerequisits

  • Download and install rust - the easiest way is using brew: brew install rust
  • Download the relevant reference genome
  • Download and install samtools - brew install samtools
  • Index the reference genome samtools faidx <path/to/downloaded/genome>

Setup

  • To build it run: cargo build
  • To run it execute: RUST_LOG=info cargo run -- <path to reference genome> <path to reference genome index> <k, e.g. 25> <number of threads to use> <path/to/output/

For example: RUST_LOG=info cargo run -- /Users/zoharetzioni/Downloads/GCF_000001405.40_GRCh38.p14_genomic.fna /Users/zoharetzioni/Downloads/GCF_000001405.40_GRCh38.p14_genomic.fna.fai 25 8 /Users/zoharetzioni/Downloads/genome-k-meriser/hg38/