All Published Workflows

VCF raw sequence reads Variant calling genetic variants gatk rust-bio-tools snakemake-wrapper-utils tabix BCFtools BWA FastQC MultiQC Pandas Picard SAMtools Snakemake Trimmomatic Variant Effect Predictor (VEP) common matplotlib numpy seaborn DNA

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

raw sequence reads Read pre-processing Report umi_tools BBMap Biopython Cutadapt FastQC MultiQC Seurat Snakemake STAR devtools dplyr ggplot2 gridExtra Matrix plotly plyr RColorBrewer stringr tidyr viridis yaml pysam scRNAseq data processing

Database metadata Peak calling Plot macs2 BEDTools Bowtie 2 DeepTools FastQC MultiQC Sambamba SAMBLASTER SAMtools Snakemake ChIP-seq

JSON raw sequence reads Variant calling genetic variants delly gatk rust-bio-tools snakemake-wrapper-utils tabix BCFtools BEDTools Bowtie 2 BWA Cutadapt FastQC fgbio FreeBayes mosdepth MultiQC Pandas Picard SAMtools Snakemake Variant Effect Predictor (VEP) vembrane numpy oschmod sklearn statsmodels Varlociraptor DNA

Expression data Peak calling Plot macs2 ataqv BEDTools Bowtie 2 DeepTools FastQC MultiQC SAMBLASTER SAMtools Snakemake ATAC-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

raw sequence reads Primer removal Quality control report dada2 BLAST cd-hit Cutadapt FastQC MultiQC Pandas PANDAseq seqtk ShortRead Snakemake Swarm VSEARCH AmpliconDuo data.table ggplot2 xtable dinopy numpy PyYAML tables Function analysis

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

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

Genome index Annotation Map BEDTools BLAST fastp FastQC GFF3 Rebase gffread HISAT2 Minimap2 RepeatMasker RepeatModeler SAMtools Snakemake StringTie RNA-Seq

JSON raw sequence reads Variant calling genetic variants delly nanofilt rust-bio-tools snakemake-wrapper-utils tabix BCFtools Biopython BWA CANU Consensus fastp FastQC fgbio FreeBayes GFFutils kallisto Kraken Krona Medaka metaspades Minimap2 MultiQC Pandas Pangolin Picard Quant QUAST SAMtools Snakemake Variant Effect Predictor (VEP) vembrane altair intervaltree numpy pysam requests Varlociraptor COVID19 Risk Mitigation