Beyond genomic variation - comparison and functional annotation of three Brassica rapagenomes: a turnip, a rapid cycling and a Chinese cabbage

Table 7 Software and scripts used in the project

Name	Running time (h)	Input format	Output format	Script purpose
cortex_var	24 / genotype	Fastq	vcf	-
*cortex_combiner	< 1	Vcf	fasta	Post-processing of cortex
*maker_pre_ws	24	Txt	Fasta	Pre-processing for MAKER
MAKER	140/genotype	Fasta	gff, fasta	-
*ortholog_assign	20/genotype	Fasta	csv, fasta	Post-processing of MAKER
NCBI BLAST	200	Fasta	xml	-
*InterProScan_ws	100	Fasta	xml	Pre-processing for Blast2GO
Blast2GO	< 1	Xml	csv	-
*run_metacyc	< 0.1	Txt	csv	Post-processing of Blast2GO
*beast_pre	< 5	Txt	nex	Pre-processing of BEAST
BEAST	24	Nex	png	-
*choose_fasta	< 0.1	Txt	Fasta	Extract sequence from fasta

The order in the table indicates the flow of the analysis, except for the script “choose_fasta” which can be used anytime when needed. Names starting with an asterisk are scripts generated specifically for this work. The script purpose column indicates when the scripts should be used before or after certain program. All scripts run under Linux and provide a short usage summary when started without arguments. “txt” input format: a list of file names used for the scripts.

ISSN: 1471-2164