A systematic comparison of error correction enzymes by next-generation sequencing

This repository contains everything needed (sans data) to generate our paper, which is openly availible on NAR. The requisite NGS data is availible at the Sequencing Read Archive

Running make all in analysis will process the raw data and generate the manuscript. The Makefile is also compatible with parallel builds.

Please note that our pipeline will use a significant amount of RAM, and will generate ~8Gb of intermediate files. Much of this comes from running the pipeline in parallel (especially the filtering steps).

Subdirectories

analysis: contains polished scripts, markdown documents, and figures

rawData: location of sequencing reads and scripts to pull them from the relevant repos

explorations: early exploratory data analysis and outdated/dead end scripts

Necessary Tools

• R and (tidyverse, broom, stringr, magrittr, data.table, dtplyr, scale, grid, gridExtra)
• Python 2.7
• uta-align or equivalently
• GNU Make
• latexmk and a reasonable LaTeX installation (ex TexLive)
• BBTools
• Bowtie2 (although not critical)