All Published Workflows

FASTQ raw sequence reads Filtering Count matrix DeepTools FeatureCounts htseqcount SAMtools Snakemake STAR RNA-Seq

JSON paired sequencing data Filtering Quality control report Biopython BLAST Consensus Cutadapt fastp Krona Pandas seqtk Snakemake DT htmltools tidyverse PyYAML taxidTools Taxonomy

Sample annotation Filtering Plot delly sniffles AnnotSV BCFtools BWA FastQC Picard Samplot SAMtools Snakemake TIDDIT SURVIVOR Trim_Galore Structural variation

TSV paired sequencing data Expression analysis Filtering Plot BEDTools Biopython Bowtie 2 Pandas SAMtools Snakemake intervaltree matplotlib networkx numpy pysam scipy seaborn De Novo

FASTQ JSON Sample ID Filtering Annotation track peddy CNVkit cyvcf2 FreeBayes Pandas SAMtools Snakemake vardict VarScan numpy pysam PyVCF PyYAML XlsxWriter Genomics

Restriction enzyme name CleanEx dataset code Filtering Plot Bowtie 2 Galaxy WorkflowHub Data identity and mapping

FASTQ-sanger raw sequence reads Filtering Report Bowtie 2 Cutadapt Galaxy MACS MultiQC SAMtools WorkflowHub Genomics

FASTQ raw sequence reads Filtering Quality control report BBMap fastp FastQC FeatureCounts kraken2 Krona Quant RNA-Seq

FASTQ raw sequence reads Filtering Quality control report BBMap Bowtie 2 fastp FastQC FeatureCounts kraken2 Krona Quant SAMtools RNA-Seq

GTF Turtle raw sequence reads Filtering Sequence assembly report fastp FastQC Genomics

FASTA FASTQ VCF Alignment Annotation Filtering Variant calling gatk tabix BCFtools Bwa-mem2 Consensus fastp illumina iVar lofreq Nextflow Pangolin Sambamba SAMtools snpEff Genomics