Our Snakemake Pipelines¶

**fragmentomics Pipeline**: A pipeline analyzing fragmentomics profile of cfDNA sequencing data. This Python Snakemake workflow focuses on: cell-free-dna, cfdna-profiling, fragment-features, fragmentomics. GitHub repository with 0 stars and 0 forks. Technologies: Snakemake, Python, bioinformatics, genomics, computational biology. **istari Pipeline**: Perform error-prone data preparation for whole genome regression modeling. This Python Snakemake workflow focuses on: covariate-validation, gwas-preparation, phenotype-validation, qc-filtering, variant-annotation. GitHub repository with 1 stars and 1 forks. Technologies: Snakemake, Python, bioinformatics, genomics, computational biology. **mpox-seek Pipeline**: A rapid pipeline for targeted and whole-genome ONT monkeypox sequencing. This Python Snakemake workflow focuses on: mamba, monkeypox, oxford-nanopore, phylogenetics, pipeline, rapid, singularity, snakemake, viral-genomics. GitHub repository with 1 stars and 0 forks. Technologies: Snakemake, Python, bioinformatics, genomics, computational biology. **pbAmp-seek Pipeline**: Identify and count PacBio Hifi amplicons. This Python Snakemake workflow focuses on: amplicon-sequencing, pacbio, snakemake-pipeline. GitHub repository with 1 stars and 2 forks. Technologies: Snakemake, Python, bioinformatics, genomics, computational biology. **DLscID Pipeline**: Deep Learning single-cell Identification and Annotation. This Python Snakemake workflow focuses on: cell-type-identification, deep-learning, single-cell-rna-seq. GitHub repository with 0 stars and 0 forks. Technologies: Snakemake, Python, bioinformatics, genomics, computational biology. **RNA-seek Pipeline**: A comprehensive quality-control and quantification RNA-seq pipeline. This Python Snakemake workflow focuses on: differential-expression-analysis, gene-expression, gene-fusions, isoform-expression, quality-control, rna-seq. GitHub repository with 5 stars and 3 forks. Technologies: Snakemake, Python, bioinformatics, genomics, computational biology. **assembly-seek Pipeline**: De novo Long-read Genome Assembly Pipeline. This Python Snakemake workflow focuses on: genome-assembly, long-read-sequencing, pacbio. GitHub repository with 2 stars and 2 forks. Technologies: Snakemake, Python, bioinformatics, genomics, computational biology. **parabricks-benchmark Pipeline**: Benchmarking parabricks GPU-accelerated tools for GATK and beyond!. This Python Snakemake workflow focuses on: benchmarking, deepvariant, gatk, germline-variants, gpu-acceleration. GitHub repository with 2 stars and 0 forks. Technologies: Snakemake, Python, bioinformatics, genomics, computational biology. **methyl-seek Pipeline**: Bisulphite-sequencing DNA methylation pipeline. This Python Snakemake workflow focuses on: bisulfite-sequencing, cell-free-dna, deconvolution, dmr. GitHub repository with 7 stars and 3 forks. Technologies: Snakemake, Python, bioinformatics, genomics, computational biology. **baseline Pipeline**: A BASE template for building pipeLINEs. This Python Snakemake workflow focuses on: documentation-template, pipeline-template, singularity, snakemake. GitHub repository with 3 stars and 1 forks. Technologies: Snakemake, Python, bioinformatics, genomics, computational biology. **leafworker Pipeline**: An awesome alternative-splicing pipeline that runs leafcutter and IsoformSwitchAnalyzeR.. This Python Snakemake workflow focuses on: alternative-splicing, covariate-correction, differential-analysis, isoform-quantification, isoform-switches. GitHub repository with 1 stars and 0 forks. Technologies: Snakemake, Python, bioinformatics, genomics, computational biology. **chrom-seek Pipeline**: An awesome set of epigenetic pipelines for bulk cfChip-seq, ChIP-seq, and ATAC-seq. This Python Snakemake workflow focuses on: annotation, atac-seq, bulk, cell-free-dna, chip-seq, differential-accessibility, differential-binding, peak-calling, quality-control. GitHub repository with 5 stars and 3 forks. Technologies: Snakemake, Python, bioinformatics, genomics, computational biology. **modr Pipeline**: An awesome Oxford Nanopore Pipeline for direct RNA-sequencing. This Python Snakemake workflow focuses on: alternative-splicing-analysis, bioinformatics, differential-expression-analysis, direct-rna-sequencing, known-transcripts, novel-transcripts, oxford-nanopore, pipeline, polya-tail-length-estimation, quality-control, rna-editing, rna-modifications, singularity, snakemake-pipeline, transcriptomics. GitHub repository with 6 stars and 1 forks. Technologies: Snakemake, Python, bioinformatics, genomics, computational biology. **iso-seek Pipeline**: An awesome pipeline for processing bulk PacBio transcriptomics data generated with ISO-seq and MAS-seq.. This Python Snakemake workflow focuses on: iso-seq, long-read-sequencing, mas-seq, pacbio-sequencing, singularity, snakemake. GitHub repository with 0 stars and 0 forks. Technologies: Snakemake, Python, bioinformatics, genomics, computational biology. **cell-seek Pipeline**: One single-cell pipeline to rule them all, one pipeline to find them, one pipeline to unify them all, and with the data bind them.. This Python Snakemake workflow focuses on: 10xgenomics, single-cell-atac-seq, single-cell-cite-seq, single-cell-omics, single-cell-rna-seq, single-cell-vdj. GitHub repository with 2 stars and 1 forks. Technologies: Snakemake, Python, bioinformatics, genomics, computational biology. **genome-seek Pipeline**: Clinical Whole Genome and Exome Sequencing Pipeline. This Python Snakemake workflow focuses on: copy-number-variation, germline-variants, hla-typing, pipeline, quality-control, singularity, snakemake, somatic-variants, structural-variants, variant-annotation, variant-effect-prediction, whole-exome-sequencing, whole-genome-sequencing. GitHub repository with 29 stars and 12 forks. Technologies: Snakemake, Python, bioinformatics, genomics, computational biology. **mir-seek Pipeline**: An awesome microRNA-sequencing pipeline. This Python Snakemake workflow focuses on: mature-mirna, micro-rna, micro-rna-expression, mirdeep2, mirna, mirna-seq, singularity, snakemake. GitHub repository with 2 stars and 1 forks. Technologies: Snakemake, Python, bioinformatics, genomics, computational biology. **metavirs Pipeline**: Viral Metagenomics Assembly and Annotation Pipeline. This Python Snakemake workflow focuses on: annotation, assembly, classification, pathogen-surveillance, pipeline, quality-control, singularity, snakemake, viral-metagenomics. GitHub repository with 6 stars and 1 forks. Technologies: Snakemake, Python, bioinformatics, genomics, computational biology. **nanite Pipeline**: A streamlined Oxford Nanopore Viral Metagenomics Pipeline . This Python Snakemake workflow focuses on: annotation, assembly, classification, pathogen-surveillance, pipeline, singularity, slim, snakemake, viral-metagenomics. GitHub repository with 6 stars and 2 forks. Technologies: Snakemake, Python, bioinformatics, genomics, computational biology. **metamorph Pipeline**: Metagenomics and Metatranscriptomics pipeline. This Python Snakemake workflow focuses on: metagenomics, metatranscriptomics, pipeline, quality-control, snakemake. GitHub repository with 5 stars and 2 forks. Technologies: Snakemake, Python, bioinformatics, genomics, computational biology. **space-seek Pipeline**: Spatial-sequencing: The final frontier. These are the voyages of the 10x Visium pipeline, space-seek.. This Python Snakemake workflow focuses on: 10xgenomics, pipeline, single-cell, singularity, snakemake, visium-hd. GitHub repository with 1 stars and 0 forks. Technologies: Snakemake, Python, bioinformatics, genomics, computational biology. **ervx Pipeline**: Endogenous Retrovirus Expression Pipeline for Human, Mouse, and Macaque for use with bulk RNA-seq. This Python Snakemake workflow focuses on: endogenous-retrovirus-expression, herv, human, mouse, pipeline, quality-control, singularity, snakemake, transposable-elements, workflow. GitHub repository with 1 stars and 1 forks. Technologies: Snakemake, Python, bioinformatics, genomics, computational biology. **mr-seek Pipeline**: Mendelian Randomization pipeline. This Python Snakemake workflow focuses on: mendelian-randomization, pipeline, snakemake. GitHub repository with 2 stars and 1 forks. Technologies: Snakemake, Python, bioinformatics, genomics, computational biology. **scErvx Pipeline**: Endogenous Retrovirus Expression Pipeline for Human and Mouse for use with data from 10x genomics (bam files). This Python Snakemake workflow focuses on: endogenous-retrovirus-expression, single-cell-rna-seq. GitHub repository with 1 stars and 0 forks. Technologies: Snakemake, Python, bioinformatics, genomics, computational biology. **cyte-seek Pipeline**: Awesome single-cell CITE-sequencing Pipeline. This Python Snakemake workflow focuses on: 10xgenomics, cite-seq, pipeline, quality-control, single-cell, singularity. GitHub repository with 2 stars and 0 forks. Technologies: Snakemake, Python, bioinformatics, genomics, computational biology. **HiIP Pipeline**: An awesome Hi-C + ChIP (HiChIP) sequencing pipeline.. This Python Snakemake workflow focuses on: chip-seq, hi-c, hichip, pipeline, singularity, snakemake. GitHub repository with 0 stars and 0 forks. Technologies: Snakemake, Python, bioinformatics, genomics, computational biology. **weave Pipeline**: An awesome BCL demultiplexing and FastQ quality-control pipeline. This Python Snakemake workflow focuses on: bcl2fastq, bclconvert, contamination-screening, disambiguate-genomes, fastp, fastq-quality-control, kaiju, kraken2, krona. GitHub repository with 1 stars and 0 forks. Technologies: Snakemake, Python, bioinformatics, genomics, computational biology. **cfChIP-seek Pipeline**: cell-free ChIP-seq pipeline. This Python Snakemake workflow focuses on: cell-free-dna, cell-type-deconvolution, chip-seq, peak-annotation, peak-calling, quality-control, snakemake. GitHub repository with 3 stars and 3 forks. Technologies: Snakemake, Python, bioinformatics, genomics, computational biology.