Files used to develop and test SLAG, Seeded Local Assembly of Genes

This dataset consists of configuration files and results files involved in developing and testing SLAG, an iterative Perl pipeline to construct local assemblies seeded on query sequences.  SLAG is intended for situations where a full genome assembly is economically or technically infeasible, and thus it emphasizes methods that can deal with shallow read depth.  SLAG and its user-runnable test suite have been deposited at https://github.com/cfcrane/SLAG.  This Dryad repository contains files that were used in preparing a manuscript, "SLAG: A Program for Seeded Local Assembly of Genes in Complex Genomes", which has been submitted to Molecular Ecology Resources.  The repository is divided into sections for scripts, simulated reads, real reads, and benchmarking against two functionally similar programs, aTRAM2 and SRAssembler.

Methods
SLAG was initially developed in 2012 under Mac OS X and further developed under RHEL5.6 and CentOS7 Linux on supercomputing clusters Coates, Halstead, and Brown at Purdue University.  Benchmarking was performed exclusively on one queue (not always the same node) on the Brown cluster.  Each benchmarking run was run by itself and was given exclusive access to the memory and 24 cores on the node.  Non-benchmarking runs shared resources with other jobs.  These trials looked at contig count, contig length, and percentage match to a reference genome from which the reads had been derived.