All Published Workflows

BAM Sample ID Mapping Report gatk tabix AdapterRemoval BCFtools BEDTools Bowtie 2 BWA fastp FastQC gatk_realigner_target_creator MapDamage MultiQC Pandas Picard QualiMap SAMtools seqtk Snakemake GLIMPSE numpy Comparative genomics

BAM SAM BEDTools Cutadapt FastQC HTSeq htseqcount SAMtools Snakemake STAR

BAM Data Transcriptome assembly Report portcullis snakemake-wrapper-utils taco Mikado pyfasta SAMtools Snakemake StringTie TransDecoder RNA

BAM CRAM FastQC MultiQC SAMtools Data quality management

BAM SAM fastp FastQC Galaxy Minimap2 MultiQC NanoPlot SAMtools WorkflowHub Genomics

BAM CPAT fastp FastQC Galaxy IsoformSwitchAnalyzeR MultiQC PfamScan STAR StringTie WorkflowHub RNA splicing

BAM Variant calling genetic variants gatk gatk_realigner_target_creator Nextflow Sambamba SAMtools RNA-Seq

BAM FASTQ raw sequence reads Alignment Pair sequence alignment BWA Bwa-mem2 fastp Nextflow SAMtools STAR RNA-Seq

BAM Map Text data Sequence clustering Map data Bwa-mem2 Galaxy MultiQC SAMtools Stacks WorkflowHub Population genomics

BAM FASTQ File format name Sequence alignment conversion Sequencing quality control File format name FastQC Galaxy Picard SAMtools WorkflowHub Sequence assembly

BAM VCF Sequence Variant calling File format name gatk BWA dbSNP Picard SAMtools Genomics

BAM Genome index Indel detection genetic variants gatk Bowtie 2 Picard SAMtools RNA-Seq