A comparison of genotyping-by-sequencing analysis methods on low-coverage crop datasets shows advantages of a new workflow, GB-eaSy

Table 2 Major steps of the 5 GBS workflows analyzed

	TASSEL-GBS	IGST	Fast-GBS	Stacks	GB-eaSy
Demultiplex reads	GBSSeqToTagDBPlugin, TagExportToTagDBPlugin	Sabre	Sabre	process_radtags	GBSX
Trim adapters	cutadapt*	trimAdaptor3.py	cutadapt	process_radtags	GBSX
Align to reference	bwa-mem*	bwa-aln	bwa-mem	bwa-mem*	bwa-mem
Call SNPs	DiscoverySNPCallerPluginV2, ProductionSNPCallerPluginV2	SAMtools/BCFtools	Platypus	pstacks, cstacks, stacks, populations	BCFtools

Each workflow uses a different series of tools to carry out read demultiplexing, adapter trimming, alignment to the reference genome, and SNP calling
*step performed manually outside the workflow

ISSN: 1471-2105