GenomeClustering

Setup

• git clone the project
• cmake . to generate Makefile
• make to make executable
• ./out/GenomeClustering <target fasta> <output path> <id> [<args>] to run the executable

Usage

usage: ./out/GenomeClustering <fasta in> <cluster out> <similarity> [<args>]

(--cache_size | -c) <size>
    Set total cache size.
(--lru | -r) <size>
    Set the size of the LRU cache.
    Behaviour undefined with --cache_size.
(--lfu | -f) <size>
    Set the size of the LFU cache.

Example use:

./out/GenomeClustering res/p3_clean_C-148-2-Caecum_S128.fa clusters.uc 0.97