使われているソフトウェア

DNA解析

ソフトウェア名	バージョン	使い方
cnvkit	0.9.10.dev0(modified)	singularity
nextflow	nextflow=21.04.0=h4a94de4_0	conda
MultiQC	v1.13.dev0(modified)	singularity
CrossMap	0.6.1	Singularity
sequenza-utils	3.0.0	Singularity
sequenza	3.0.0	Singularity
parabricks	3.5.0	SHIROKANE の moduleコマンド
singularity	3.7.0	SHIROKANE の moduleコマンド
GenomonPipeline	2.6.3(一部のツールmodified)	パス指定
GenomonSV	0.6.1b1(modified)	singularity
sv_utils	0.5.1(modified)	singularity
GenomonFisher	0.2.0	singularity
GenomonMutationFilter	0.2.1(modified)	singularity
GenomonMutationAnnotation	0.1.0	singularity
MutationUtil	0.5.0	singularity
genomon_Rscripts	v0.1.3	singularity
GenomonPostAnalysis	v1.4.1	singularity
paplot	v0.5.5	singularity
MSIsensor-pro	1.2.0(fixed)	Singularity
ITD Assembler	modified	Singularity
fastqc	docker://biocontainers/fastqc:v0.11.8dfsg-2-deb_cv1	Singularity
Manta	docker://quay.io/biocontainers/manta:1.6.0–py27_0	Singularity
GRIDSS	docker://gridss/gridss:2.12.0 (modified)	Singularity
FACETS	0.6.2(fixed)	Singularity
NGSCheckMate	1.0.0	Singularity
MIMcall	modified	Singularity
GATK	4.1.0.0	Singularity
CHORD	2.0.0	Singularity
picard	2.25.0	Singularity
Bowtie2	2.4.4	Singularity
SurVirus		Singularity
ascatNgs	docker://quay.io/wtsicgp/dockstore-cgpwgs:2.1.1	Singularity
hyperclust	(modified)	Singularity
cgpPindel	docker://quay.io/wtsicgp/cgppindel:3.10.0	Singularity
scarHRD		Singularity
battenberg	2.2.10(modified)	Singularity
Strelka2	2.9.10	Singularity

RNA解析

ソフトウェア名	バージョン	使い方
nextflow	nextflow=21.04.0=h4a94de4_0	conda
singularity	3.7.0	SHIROKANE の moduleコマンド
STAR	docker://trinityctat/starfusion:1.10.1	singularity
STAR-Fusion	docker://trinityctat/starfusion:1.10.1	singularity
DESeq2	1.34.0	singularity
Htseq	2.0.1	singularity
picard	2.25.0	Singularity
NGSCheckMate	1.0.0	Singularity
GenomonExpression	0.4.0(modified)	singularity
fusionfusion	0.4.0(modified)	singularity
fusion_utils	0.2.0(modified)	singularity