Reimplementation of demix_check using GNU coreutils. This repository provides scripts to perform the steps to set up the demix_check reference and check reads binned with mGEMS without requiring the python or R dependencies in the original.
Version numbers are for versions that have been tested. Older or newer versions should also work.
If the dependencies are not installed on your system, run the supplied install.sh script to install them from
source (requires a C/C++ compiler). After running the script, you will
need to export the paths to these tools by
running the following command in the directory where simple-demix_check is installed before running the scripts:
export PATH=$PATH:$(pwd)
nthreads=4
memmegas=1024M
tmpdir=tmp
setup_reference.sh --ref_info ref_info.tsv --threads $nthreads --tmpdir $tmpdir --bufsize $memmegas
cluster_name=lineage-0
abundances=cluster_abundances.txt nthreads=4 memmegas=1024M
tmpdir=tmp ref_dir=setup_reference_output forward=reads_1.fastq.gz
reverse=reads_2.fastq.gz
check_reads.sh --cluster $cluster_name --abundances $abundances --threads $nthreads --tmpdir $tmpdir --bufsize $memmegas --reference $ref_dir --fwd $forward --rev $reverse
simple-demix_check is licensed under the BSD-3-Clause license. A copy of the license is supplied with the project, or can alternatively be obtained from https://opensource.org/licenses/BSD-3-Clause.