DOI: 10.5061/dryad.0p2ngf22s
title: Files used to develop and test SLAG, Seeded Local Assembly of Genes

description: 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.
description: 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.
description:       This repository is a gzipped
 "tarball" that can be downloaded, uncompressed, and expanded to
 reveal a directory tree rooted on todryad, with subdirectories
 simulations, realdata, benchmarking, and scripts.  The simulations
 involved simulated reads extracted from random sites in three homoeologous
 regions of chromosomes 1A, 1B, and 1D in the International Wheat Genome
 Sequencing Consortium version 2.0 assembly of wheat variety 'Chinese
 Spring'; see the deflines in
 simulations/configs/cutoutregionforreadsimulations.fasta for coordinates. 
 The simulated reads fell into three groups by length, short (2x150 bp
 paired ends with error frequencies similar to Illumina), middle (400-600
 bp with low error frequencies), and long (3500 - 14000 bp with ca. 10%
 error frequencies similar to Oxford Nanopore several years ago).  These
 groups are denoted as SR, MR, and LR in the configuration and resulting
 subset.contigs files. The latter contain local assemblies that match the
 seeding sequence, and scripts collected information about contig count,
 length, and percent nucleotide matching to the parent genome assembly as
 found by blastn alignment.        The real reads were
 quality-filtered from 18 Genbank SRA accessions, ERR3288286 through
 ERR3288295, which are Pacbio reads from maize B73, and ERR3288215 through
 ERR328818, which are paired-end Illumina reads from maize B73. The
 resulting local assemblies were aligned to the published B73 genome
 (Genbank accession GCF_000005005.2).        The benchmarking directory
 includes local assemblies produced with the simulated wheat reads and real
 maize Illumina reads against a panel of 10 maize enzymes, where each
 enzyme was represented by 2-7 accessions from Genbank nr: cellulose
 synthase (NP_001104955.2, NP_001104956.2, NP_001104959.2, NP_001105236.2,
 NP_001105574.1, NP_001105672.1, NP_001292792.1), ferredoxin
 (NP_001104851.1, NP_001136908.1, NP_001150750.1, NP_001336742.1,
 XP_020394593.1, XP_020405634.1), hexokinase (NP_001123599.1,
 XP_008672065.1, XP_008674565.1, XP_008675068.1), histone deacetylase
 (NP_001104901.1, NP_001105402.2, XP_008673398.1, XP_008677775.1,
 XP_020396306.1), isocitrate dehydrogenase (AQK53344.1, AQK89292.1,
 AQK97039.1, AQK88693.1, NP_001295424.1, ONM16007.1, ONM58401.1),
 peptidylprolylisomerase (AQK62104.1, AQK70996.1, AQL06400.1, ONM03151.1,
 ONM04876.1, ONM54033.1), phosphoglucoisomerase (NP_001105368.1,
 XP_008651420.1), phosphoglucomutase (NP_001105405.1, NP_001105703.1,
 XP_008675355.1, XP_020395615.1), sucrose synthase (XP_008645119.1,
 XP_008679107.1, XP_020399433.1, XP_023156234.1), and transaminase
 (NP_001149818.2, NP_001278682.1, XP_008645517.1, XP_008668890.1,
 XP_008672129.1).  Runtimes and memory usage were recorded and output with
 Slurm utility sacct in the file
 benchmarking/runtimes/benchmarkrunrecords.txt, which covers the interval
 from 31 January 2021 through 10 June 2021.  Benchmarking jobs were
 systematically named with structure AABBCCCDDD.sh, where AA is one of ra
 (aTRAM2), rs (SLAG), or rr (SRAssembler); BB is Ta for wheat or Zm for
 maize; CCC is three letters for the enzyme activity (cel = cellulose
 synthase, fer = ferredoxin, hex = hexokinase, his = histone deacetylase,
 iso = isocitrate dehydrogenase, pep = peptidylprolylisomerase, pgi =
 phosphoglucoisomerase, pgm = phosphoglucomutase, suc = sucrose synthase,
 tra = transaminase); and DDD is three letters for the assembler, such as
 spa for SPAdes or cap for cap3.  Some jobs ran more than once before a
 successful run.  Each line in the file has sacct fields User, JobID,
 Jobname%40, partition, state, time, start, end, elapsed, MaxRss,
 MaxVMSize, MaxPages, TotalCPU, nnodes, ncpus, and nodelist. 
       Subdirectory scripts also includes a much older (pre-2015)
 set of scripts based on an early version of SLAG, which was called
 localassembly0215.pl.  These scripts were used to investigate local
 assembly of multiple alleles of a gene across an invariant central region,
 which ultimately gave rise to Figure 12 in "SLAG: A Program for
 Seeded Local Assembly of Genes in Complex Genomes".