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Table 7 Software and scripts used in the project

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

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
  1. 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.