Templates

A bunch of templates for processing HTS data. Particularly useful for using with nextflow pipelines.

Quick reference

process_assembly_mapping.py - Processes the coverage report and checks assembly filters from the assembly_mapping process. [changelog, API]
mapping2json.py - exports results from a samtool depth file to a json file that contains a key:value such as accession number:coverage .
mashdist2json.py - exports results from mash dist to a json file that contains a key:value such as accession number:distance .
mashscreen2json.py - exports results from mash screen to a json file that contains a key:[values] such as accession number:[copy number, identity] .

git submodule add https://github.com/ODiogoSilva/templates.git templates

git submodule foreach git pull origin master

Name		Name	Last commit message	Last commit date
Latest commit History 280 Commits
assemblerflow_utils		assemblerflow_utils
.gitignore		.gitignore
README.md		README.md
__init__.py		__init__.py
assembly_report.py		assembly_report.py
fastqc.py		fastqc.py
fastqc_report.py		fastqc_report.py
integrity_coverage.py		integrity_coverage.py
mapping2json.py		mapping2json.py
mashdist2json.py		mashdist2json.py
mashscreen2json.py		mashscreen2json.py
megahit.py		megahit.py
metaspades.py		metaspades.py
pATLAS_consensus_json.py		pATLAS_consensus_json.py
pipeline_status.py		pipeline_status.py
process_abricate.py		process_abricate.py
process_assembly.py		process_assembly.py
process_assembly_mapping.py		process_assembly_mapping.py
skesa.py		skesa.py
spades.py		spades.py
trimmomatic.py		trimmomatic.py
trimmomatic_report.py		trimmomatic_report.py