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How To Install RADseq SNP-calling Software On A Linux Supercomputer

Justin C. Bagley, February 12, 2018, Richmond, VA, USA

Below, you will find a series of steps for installing on Linux three of the main software programs used for de novo assembly and SNP calling from RADseq-type next-generation sequencing data (given in no particular order): 1) ipyrad (Eaton 2014; Eaton and Overcast 2016), 2) dDocent (Puritz et al. 2014), and 3) Stacks v2.0beta (Catchen et al. 2013), and their dependencies. We will install all three because, even though a given RADseq paper will inevitably present results based on SNPs gleaned mainly from using one of these programs, Stacks is a dependency of dDocent and it is a good idea to compare results from multiple assemblers to ensure they converge on a similar number of SNPs.

As in my other Gists, "$" in the code below references the Linux prompt, which is not to be typed if following along with me. Within code snippets, lines just below a line starting with

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Keybase proof

I hereby claim:

• I am justincbagley on github.
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• I have a public key ASCxJVNMZzqQcBR8GRqlRF6noG-EgEvy0fGe0Qa3A-yXbAo

To claim this, I am signing this object:

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Queue check function for godel

December 19, 2019

Justin C. Bagley, Ph.D.
University of Missouri-St. Louis (UMSL)
Virginia Commonwealth University (VCU)

myq

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Install nQuire Software

nQuire is a software program (Weiß et al. 2018) that estimates sample ploidy levels from next-generation sequencing (NGS; e.g. Illumina) reads for one or multiple samples, starting from BAM file(s) (extension '.bam'; Li et al. 2009) for the sample(s). It is assumed that the .bam input file(s) were output by an aligner such as bwa (Li and Durbin 2009) and contain information on reads mapped to an appropriate reference (draft reference genome, pseudo-reference genome assembly, etc.). Find the nQuire paper here or using the reference below.

nQuire is available through a GitHub repository, and installation instructions are given in the main README for the repo. I have had success installing nQuire, following the given instructions, on both macOS High Sierra v10.13+ and CentOS 6/7 Linux OS's.

INSTALL nQuire

git clone --recursive https://github.com/clwgg/nQuire

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For those interested in running RAxML for phylogenetic inference using maximum-likelihood, here is a little function for cleaning up (within a RAxML run directory) after a failed RAxML run. Just add the following function to your ~/.bash_profile (on Mac) or ~/.bashrc (on Linux supercomputer) and do source ~/.bash_profile (or simliar) to have it on hand from the cli.

## CLEAN RAXML RUN DIR (TO CLEAN UP AFTER FAILED RUNS, BEFORE RESUBMITTING TO QUEUE)

clean_raxml () {
        rm ./*.txt; rm ./*.reduced; rm ./RAxML_info* ;
}

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dDocent Utility Shell Scripts

Justin C. Bagley, Ph.D.

University of Missouri-St. Louis

This Gist provides a handful of utility shell scripts for use with dDocent, which I wrote in March 2020. Specifically, these scripts are meant to be placed in dDocent run subfolders, in order to provide means of quickly cleaning up the workspace after failed or stopped (ctrl + C) runs. They are sufficiently generic to clean any dDocent run folder, and they range from a minor clean to a deep clean (removes essentially everything generated during run).

Files

• deep_clean_ddocent_folder.sh

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Reasons to Prefer Commalind Line Interface (CLI) Software to GUIs

One common question, upon seeing someone working in a terminal is,

"Why don't you use a nice-looking, easy-to-use GUI software instead?"

And a perrenial related question discussed among developers is along the lines of,

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PartitionFinder Citations

v1.1.0 manual:

• Lanfear, R., 2013. PartitionFinder v1.1.0 and PartitionFinderProtein v1.1.0 Manual. Available from: http://www.robertlanfear.com/partitionfinder.

v1.1.0 software:

• Lanfear, R., Calcott, B., Ho, S.Y. and Guindon, S., 2012. PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Molecular Biology and Evolution, 29(6), 1695-1701.

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The Markdown Rendering Quest Continues

GitHub Markdown

Everyone loves GitHub-flavored Markdown. A problem of interest for some time now is rendering, editing, and saving Markdown with GitHub rendering style.

This is something that has interested me since at least 2018. Indeed, I have been using grip for Markdown preview, conversion, and saving to PDF on macOS for years, as I detailed previously in one of my other popular Gists here.

Problem: GitHub API Limits

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zipper

A useful function to add to your ~/.bash_profile or ~/.bashrc file on macOS that automates custom zipping of files and folders. This function also checks to make sure that the resulting gzipped folder has the same date as the last date of modificationf or the folder.

Add in your path as a full shell script by copying all below and saving into a file named zipper located in your $PATH (e.g. /usr/bin), or copy and paste just the function into ~/.bash_profile or ~/.bashrc then restart Terminal.

#!/bin/sh

# zipper