Kmer Mapper

Python package for fast mapping of kmers from a fasta file to a Kmer Index. Relies on Numpy and some Cython to achieve fast mapping.

Installation

Requires Python 3.

pip install kmer_mapper

Usage

Kmer mapper works with .fa and .fq files (also gzipped).

kmer_mapper map -i kmer_index.npz -f reads.fa -o results --n-threads 10 --kmer-size 31

GPU-support (experimental)

You should have a GPU with 4 GB or more memory. You may adjust the chunk size to lower the memory usage.

kmer_mapper map -i kmer_index.npz -f reads.fa -o results --n-threads 10 --kmer-size 31 --gpu True --chunk-size 10000000