Snakemake and Snaketool pipeline to taxonomically profile ONT long read metagenomics.
Snakemake and Snaketool pipeline to taxonomically profile ONT long read metagenomics with sourmash
Much code and ideas have been taken and adapted from the pb-metagenomics-tools repository.
Additionally this pipeline has been substantially informed by this benchmarking study.
Assumes that your reads are in a directory, fastq.gz
suffixed.
git clone "https://github.com/gbouras13/metamash.git"
cd metamash/
pip install -e .
metamash --help
metamash install --help
metamash run --help
Steps:
- Download the CHM13
human-t2t-hla.fa
host genome (from hostile) with the following command.
metamash install --database host_genome_db
- Run trimnami specifying the directory of FASTQ reads as
--reads
ensuring the mapping is for ONT
trimnami run --reads metamash/test_data --host host_genome_db/human-t2t-hla.fa --minimap map-ont --output trimnami_output nanopore
You will find the host depleted and trimmed reads in <output>/nanopore
so here e.g. trimnami_output/nanopore
.
- Download the mmseqs2 v 13.45111 uniref50 database - this takes ages in Australia~
e.g.
# will write to 'uniref50' directory
mmseqs databases UniRef50 uniref50 tmp --threads 3
- Run metamash