All Published Workflows

JSON User metadata Expression analysis Quality control report bedGraphToBigWig BEDTools Cutadapt FastQC MultiQC Quant Salmon SAMtools Snakemake STAR Trim_Galore RNA-Seq

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 raw sequence reads Sequencing quality control Haplotype map gatk BWA FastQC MultiQC Snakemake Trim_Galore Genomics

snpsplit Biopython bsseq BWA DSS GenomicRanges HISAT2 nanopolish SAMtools Snakemake Bismark broom data.table dplyr magrittr readr tidyverse numpy pysam Trim_Galore

miranda BEDTools Biopython gtftogenepred HISAT2 Quant Salmon SAMtools Snakemake tidyverse oschmod Trim_Galore

raw sequence reads Quantification Quality control report BWA FastQC gffread GFFutils HTSeq htseqcount kallisto MultiQC QualiMap Quant RSEM Salmon SAMtools Snakemake STAR Trim_Galore Gene expression

gatk tabix DeepTools FastQC MultiQC Quant Salmon SAMtools seqtk Snakemake SortMeRNA STAR vt Trim_Galore

JSON hla-la Biopython BWA Bwa-mem2 Diamond Pandas Picard SAMtools Snakemake STAR oschmod Trim_Galore

BEDTools BiocParallel Cutadapt dmrseq FastQC MultiQC QualiMap SAMtools Snakemake Bismark data.table stringr Trim_Galore

bedGraphToBigWig Biopython DeepTools FastQC SAMtools Snakemake Bismark Trim_Galore

BSgenome.Hsapiens.UCSC.hg38 BSgenome.Mmusculus.UCSC.mm10 TxDb.Hsapiens.UCSC.hg38.knownGene TxDb.Mmusculus.UCSC.mm10.knownGene macs2 Rsamtools ATACseqQC bedGraphToBigWig BEDTools Bowtie 2 FastQC GenomicAlignments GenomicScores SAMtools Snakemake STAR ggplot2 Trim_Galore

BEDTools Bowtie 2 FastQC homer Kraken kraken2 Krona MultiQC Picard SAMtools Singularity Hub Snakemake Bismark Trim_Galore