All Published Workflows

raw sequence reads Alignment Sequence alignment report macs2 ucsc-bedclip bedGraphToBigWig BEDTools BWA Picard SAMtools Snakemake

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

raw sequence reads Alignment Feature table cooler BWA Pairix SAMtools Snakemake Sequence analysis

Data Alignment Count matrix rustybam BEDTools mrsFAST Pandas SAMtools seqtk Snakemake fastCN numba pysam Data quality management

Alignment cialign gff2bed snakemake-wrapper-utils tabix BCFtools Biopython IQ-TREE MAFFT API (EBI) Minimap2 Pandas SAMtools seqtk Snakemake subSeq Variant Effect Predictor (VEP) pysam Sequence analysis

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

raw sequence reads Alignment Report BWA DeepTools FastQC MultiQC SAMtools Snakemake ChIP-seq

FASTQ Sample ID Alignment Annotation track Snakemake pysam XlsxWriter Genetics

BAM FASTQ raw sequence reads Alignment Pair sequence alignment BWA Bwa-mem2 fastp Nextflow SAMtools STAR RNA-Seq

FASTQ raw sequence reads Alignment Quality control report manta StructuralVariantAnnotation BEDTools BWA CODEX ExomeDepth fastp FastQC GRIDSS SAMtools VariantAnnotation stringr Protein variants

FASTQ raw sequence reads Alignment Genome index BWA Cutadapt Picard SAMtools Structural 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