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README.md

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] .

How to use as a submodule

Add templates to your project

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

Update templates on your project

git submodule foreach git pull origin master
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