Docker

The folder of docker containers files

• abra2
  • ABRA 2.20
  • samtools 1.10
• bcl2fastq
  • Convert BCL to Fastq
• dna_alignment
  • bwa 0.7.17
  • fgbio 1.1.0
  • picard 2.21.7
  • process_scripts
  • samtools markdup
  • picard Picard MarkDuplicates
  • picard_umi Picard MarkDuplicates BARCODE_TAG=RX
  • fgbio_umi GroupReadsByUmi, CallMolecularConsensusReads
• profiling_qc
  • fastqc
  • coveragebed
  • samtools flagstat
  • picard EstimateLibraryComplexity
  • process_scripts
• rna_alignment
  • hisat2
• rna_gene_abundance
  • StringTie
  • FeatureCount
• starfusion
  • StarFusion
• structuralvariant
  • pindel: PINDEL
  • pindel_itd: PINDEL restricted to itd_genes.bed
  • delly: DELLY
  • svaba: SVABA
  • cnvkit: CNVKit
  • itdseek: ITDSeek
• trim_galore
  • trim_galore_v0.4.1
  • cutadapt==1.9.1
  • process_scripts
• variantcalling
  • fb: FreeBayes
  • platypus: Platypus
  • strelka2: Strelka2
  • mutect: MuTect2 (GATK4)
  • shimmer: Shimmer