Membership matrix example

This example shows how to build a k-mer count matrix from 2 samples, D1 and D2.

data
├── 1.fasta
├── 2.fasta
└── kmtricks.fof

> cat data/kmtricks.fof
D1: data/1.fasta
D2: data/2.fasta

Build matrix

kmtricks pipeline --file ./data/kmtricks.fof     \
                  --run-dir ./membership_example \
                  --mode kmer:pa:bin             \
                  --hard-min 2                   \
                  --lz4

Exploit matrix

Each sub-matrix can then be processed thanks to kmtricks API or they can be aggregated using kmtricks aggregate:

kmtricks aggregate --pa-matrix kmer --format text --lz4-in > final_matrix.txt # Concatenate sorted partitions
kmtricks aggregate --pa-matrix kmer --format text --lz4-in --sorted > final_matrix.txt # whole matrix is sorted

Sub-matrices can also be directly dumped into text by replacing --mode kmer:pa:bin by --mode kmer:pa:text.