All Published Workflows

FASTQ Sample ID Alignment Count matrix Minimap2 Quant Salmon SAMtools Snakemake stageR dplyr ggplot2 tidyr Gene expression

FASTQ Sample ID Mapping Taxonomy ngs_te_mapper2 trim-galore RelocaTE2 Snakemake TEMP TEMP2 Whole genome sequencing

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

Sample ID Sequencing quality control Quality control report BBMap Cutadapt fastp Pandas Snakemake Trimmomatic matplotlib Quality affairs

Sample ID Analysis Text data BEDTools Minimap2 SAMtools Snakemake Sequence analysis

Sample ID Analysis Report macs2 bedGraphToBigWig BEDTools Bowtie 2 BWA DeepTools FastQC homer Pandas Sambamba SAMtools Snakemake Trimmomatic ATAC-seq

FASTQ Sample ID Genome assembly Ontology mapping Bowtie 2 edgeR FeatureCounts metagenomeSeq MultiQC Pandas SAMtools Snakemake metagenomics

Sample ID Peak calling Gene expression matrix FiMO Pandas SCANPY Snakemake renv numpy scipy SEACells tqdm ChIP-seq

Sample ID Allele frequency distribution analysis genetic variants tabix Snakemake optparse numpy pysam GWAS study Population genomics

FASTQ Sample ID Alignment Annotation track Snakemake pysam XlsxWriter Genetics

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

Sample ID Peak calling Plot macs2 bedGraphToBigWig SAMtools Snakemake Genomics