Scripts for post-processing of output from the ATLAS pipeline, approx. version 2.14 and higher
Copyright Jackson M. Tsuji, 2023
ATLAS is an open-source and extendable pipeline for metagenomic analysis. This repo contains a collection of helper scripts to perform post-processing on ATLAS output.
Scripts are available in the scripts directory and can be run from the Linux command
line. Try running the script with the -h flag to get usage and install instructions.
Scripts contained in this repo include:
generate_MAG_table.py: generates something like an OTU-table (in amplicon sequencing) for genome bins output by ATLAS. Requires Python3 and the pandas package. Default settings are optimized for ATLAS 2.14 (approx.) and higher. NOTE: revert to version 0.1.0 for use with older ATLAS2 versions (e.g., v2.2.0). Requires at least Python 3.6.