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