StructuralGenomeVariations

Comparison of tools for the identification of structural variations in microbial genomes

Name	Name	Last commit message	Last commit date
Latest commit vrohnie switched clove latest build from git code Aug 29, 2023 4bce8c5 · Aug 29, 2023 History 115 Commits
bdmax	bdmax	Adding 10th entry to VCF header in transformation scripts	Jan 10, 2023
breseq	breseq	Added header line to Breseq vcf	Mar 8, 2023
clove	clove	switched clove latest build from git code	Aug 29, 2023
clovebiotech	clovebiotech	exclude delly from clove and clovebiotech	Aug 8, 2023
cortex	cortex	added tool WHAM	Aug 31, 2022
delly_0.7.9	delly_0.7.9	set user to root for bcftools	Aug 8, 2023
delly_1.1.6	delly_1.1.6	added convert step for delly_0.7.9	Aug 8, 2023
dysgu	dysgu	fixing time logging	Sep 13, 2022
evaluation	evaluation	switched clove to version 0.16	Aug 16, 2023
gridss	gridss	fixing time logging	Sep 13, 2022
lumpy	lumpy	added thread option where possible	Sep 13, 2022
manta	manta	fixing time logging	Sep 13, 2022
metasv	metasv	added tool WHAM	Aug 31, 2022
pindel	pindel	added thread option where possible	Sep 13, 2022
softsv	softsv	Adding 10th entry to VCF header in transformation scripts	Jan 10, 2023
sv_sim	sv_sim	switched clove latest build from git code	Aug 29, 2023
svaba	svaba	added thread option where possible	Sep 13, 2022
wham	wham	added thread option where possible	Sep 13, 2022
README.md	README.md	filepaths	Aug 16, 2022
callSvBreseq.sh	callSvBreseq.sh	adapted callSvBreseq to downsample fastq files	Apr 12, 2023
callSvFromBam.sh	callSvFromBam.sh	switched way to determine actual ref fasta	Aug 9, 2023
callSvFromFastq.sh	callSvFromFastq.sh	new script for breseq only	Dec 5, 2022
doall.sh	doall.sh	chmod	Aug 16, 2022
doit.sh	doit.sh	making two different delly docker versions	Aug 8, 2023
log_eval.sh	log_eval.sh	mv log_eval	Aug 16, 2022
mapping.sh	mapping.sh	chmod	Aug 16, 2022

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