From 99b3f14677b727ba9de54aac2b1ea5d33bbbd2ba Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Wed, 21 Apr 2021 12:10:13 -0600 Subject: [PATCH] README formatting --- README.md | 57 +++++++++++++++++++++++++++++++++++++------------------ 1 file changed, 39 insertions(+), 18 deletions(-) diff --git a/README.md b/README.md index 413d651..145e62b 100644 --- a/README.md +++ b/README.md @@ -4,9 +4,15 @@ # Cow/calf Rumen Metagenomics Pipeline -An end-to-end script to convert Illumina shotgun sequences and metadata into full-blown diversity tables and visualizations. Of course, it's focused on the rumen and dam/calf relationships, but is widely applicable to other systems. +An end-to-end script to convert Illumina shotgun sequences and metadata into +full-blown diversity tables and visualizations. Of course, it's focused on the +rumen and dam/calf relationships, but is widely applicable to other systems. -Written entirely during Spring Semester 2019 for work done in [Dr. Hannah Cunningham-Hollinger's lab][hollinger-lab] at the University of Wyoming, computed on UW's [ARCC High-performance servers][arcc-servers] and presented as a [poster] at the Western Section American Association of Animal Science annual meeting. +Written entirely during Spring Semester 2019 for work done in [Dr. Hannah +Cunningham-Hollinger's lab][hollinger-lab] at the University of Wyoming, +computed on UW's [ARCC High-performance servers][arcc-servers] and presented as +a [poster] at the Western Section American Association of Animal Science annual +meeting. ## Prerequisites @@ -17,7 +23,8 @@ You will need access to the following commands/programs: - `source activate` ([Miniconda]) - `qiime`, `biom` (Install within [conda environment] named `qiime2`) -If working on a HPC, contact your department to find out how to get access to these commands. +If working on a HPC, contact your department to find out how to get access to +these commands. ## Usage @@ -27,7 +34,12 @@ Clone the script files git clone https://github.com/MillironX/cowcalf-rumen-metagenomic-pipeline.git ``` -Create a directory with all forward- and reverse- read files in it, named as `_R1_001.fastq.gz` for forward-reads and `_R2_001.fastq.gz` for reverse-reads. Add a [QIIME2-compatable metadata file][qiime2-metadata] named `metadata.tsv`, text files containing the minimum and maximum rarefaction values names `rarefaction.min.txt` and `rarefaction.max.txt` and copy all of the code files into it. It should look like +Create a directory with all forward- and reverse- read files in it, named as +`_R1_001.fastq.gz` for forward-reads and `_R2_001.fastq.gz` +for reverse-reads. Add a [QIIME2-compatible metadata file][qiime2-metadata] +named `metadata.tsv`, text files containing the minimum and maximum rarefaction +values names `rarefaction.min.txt` and `rarefaction.max.txt` and copy all of the +code files into it. It should look like ```plaintext . @@ -51,7 +63,11 @@ Create a directory with all forward- and reverse- read files in it, named as `