All Published Workflows

FASTQ-illumina Query script Genome assembly Taxonomic classification tabix BCFtools BEDTools breseq BWA Consensus FastQC FreeBayes iVar kraken2 Pangolin QUAST SAMtools Snakemake vt Trim_Galore COVID19 Risk Mitigation

FASTQ-illumina bacterial Genome assembly Sequence assembly report rasusa BWA CANU Diamond Filtlong Flye Medaka Minimap2 pilon proovframe Racon Raven SAMtools Snakemake Unicycler nanopore

FASTQ-illumina JSON Sample annotation Variant calling genetic variants snakemake-wrapper-utils EnhancedVolcano BCFtools DESeq2 fastp FreeBayes GLUE HISAT2 kallisto mosdepth MultiQC Pandas pheatmap Quant SAMBLASTER SAMtools sleuth Snakemake snpEff Vcflib data.table dplyr ggplot2 ggrepel jsonlite openxlsx RColorBrewer tidyverse ipykernel matplotlib matplotlib-venn numpy papermill pop-tools scipy zarr Population genomics

FASTQ-illumina raw sequence reads Alignment Quality control report FastQC MultiQC Snakemake Function analysis

FASTQ-illumina JSON raw sequence reads Sequence read processing Quality control report preseq Arriba Bowtie 2 Cutadapt FastQC gtftogenepred kraken2 Krona MultiQC Picard QualiMap RSEM SAMtools Snakemake STAR Telescope Gene expression

FASTQ-illumina raw sequence reads RNA-Seq quantification Quality control report BBMap Cutadapt FastQC gffread HTSeq htseqcount MultiQC Quant Salmon SAMtools STAR RNA-Seq

FASTQ-illumina raw sequence reads Quantification genetic variants ABRicate FastQC kallisto metaprokka Minimap2 MMseqs Nextflow Quant SAMtools TransDecoder metagenomics

FASTQ-illumina raw sequence reads Mapping Quality control report BEDTools Cufflinks Cutadapt Galaxy MultiQC STAR WorkflowHub RNA-Seq

FASTQ-illumina FASTQ-sanger raw sequence reads Peak calling Report Bowtie 2 Cutadapt Galaxy illumina MACS MultiQC SAMtools WorkflowHub Biological databases

FASTQ-illumina raw sequence reads Sequencing quality control Quality control report Galaxy Quality Assessment WorkflowHub Genomics

FASTQ-illumina raw sequence reads Variant calling genetic variants tabix BCFtools Bowtie 2 Consensus FastQC lofreq Picard SAMtools Trimmomatic Sequence analysis

FASTQ-illumina JSON raw sequence reads Sequencing quality control genetic variants prodigal virsorter BLAST chromoMap fastp FastQC hmmscan (EBI) Krona MashMap MultiQC SPAdes ggplot2 magrittr plotly viral-genomics