使われているソフトウェア
======================================

DNA解析
^^^^^^^^^

.. csv-table::
   :header: ソフトウェア名, バージョン, 使い方
   :widths: 11, 11, 11

   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
^^^^^^^^^

.. csv-table::
   :header: ソフトウェア名, バージョン, 使い方
   :widths: 11, 11, 11

   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