metag-pipeline

This is the pipeline Adina is using for the MSU HPC. Its fairly automated but does not include:

Name		Name	Last commit message	Last commit date
Latest commit History 20 Commits
.gitignore		.gitignore
LICENSE		LICENSE
README.md		README.md
assembly-pipeline.sb		assembly-pipeline.sb
assembly-pipeline.sh		assembly-pipeline.sh
bedcoverage-to-coverage.py		bedcoverage-to-coverage.py
blast-pipeline.sh		blast-pipeline.sh
card-pipeline.sh		card-pipeline.sh
check-for-both-pairs.py		check-for-both-pairs.py
count-hits.py		count-hits.py
count-up-from-reads.py		count-up-from-reads.py
coverage-bed-reference.py		coverage-bed-reference.py
fastq-to-fasta.py		fastq-to-fasta.py
mapping-pipeline.sh		mapping-pipeline.sh
merge.py		merge.py
pre-assembly-wrangle.sh		pre-assembly-wrangle.sh
sam-to-coverage.py		sam-to-coverage.py
trimming-pipeline-slurm.sb		trimming-pipeline-slurm.sb
trimming-pipeline.sh		trimming-pipeline.sh

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