All Published Workflows

181 workflows that have been reviewed and published

dna-seq-gatk-variant-calling
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This Snakemake pipeline implements the GATK best-practices workflow
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public

This Snakemake pipeline implements the GATK best-practices workflow for calling small germline variants. The usage of thi...
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
Free
57
hamronization_workflow
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Harmonization of AMR predictor tool outputs
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public

hAMRonization is a project aiming at the harmonization of output file formats of antimicrobial resistance detection tools. Th...
ABRicate AMRFinderPlus ariba prodigal srst2 BLAST BWA GROOT hmmsearch (genouest) KMA SAMtools seqkit Snakemake sraX Trimmomatic DeepARG v2.0 hAMRonization oschmod RGI
Free
49
nbis-meta
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A snakemake workflow for metagenomic projects
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public

A workflow for metagenomic projects A snakemake workflow for paired- and/or single-end whole-genome shotgun metagenomic d...
Barrnap prodigal MEGAHIT Biopython BLAST Bowtie 2 Centrifuge CheckM contigtax Cutadapt edgeR eggNOG-mapper v2 FastANI FastQC FeatureCounts Infernal cmscan (EBI) kraken2 Krona MaxBin MetaBAT 2 metagenomeSeq MetaPhlAn metaspades MultiQC Pandas Picard SAMtools seqtk Snakemake SortMeRNA SqueezeMeta Trimmomatic Trnascan-SE CONCOCT common gtdbtk networkx numpy RGI
Free
137
eukheist
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EukHeist: Capturing environmental eukaryotic genomes
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public

Molecular and genomic approaches, particularly those applied to whole, mixed communities (e.g. metagenomics, metatranscriptom...
eukrep prodigal MEGAHIT BWA FastQC MetaBAT 2 MultiQC SAMtools Snakemake Trimmomatic
Free
16
tapseq_manuscript
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Analysis code for the TAP-seq manuscript.
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public

This repository contains code to reproduce the results presented in the article. It builds upon a snakemake workflow that...
bigWig ucsc-liftover BiocParallel Biopython Biostrings BSgenome Consensus GenomicAlignments GenomicFeatures GenomicRanges HiTC Pandas Picard rtracklayer SAMtools Snakemake STAR Trimmomatic corrplot eulerr factoextra GGally ggplot2 ggpubr ggrepel gridExtra here kableExtra Matrix optparse plotly pROC readxl tidyverse numpy plotly
Free
210
pacman-pipeline
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Bioinformatics pipeline for the analysis of amplicon sequencing data of eDNA samples from the PacMAN project
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public

This is the bioinformatics pipeline developed for the PacMAN (Pacific Islands Marine Bioinvasions Alert Network). This pipeli...
JSON dada2 Biopython Biostrings BLAST Bowtie 2 Cutadapt FastQC MultiQC phyloseq seqtk Snakemake subSeq Trimmomatic dplyr ggplot2 plyr stringr tibble tidyr worrms xml2 yaml
Free
27
clin-mngs
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Clin-mNGS: Automated pipeline for pathogen detection from clinical metagenomic data
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public

The Clin-mNGS pipeline is an integrated, open-source, scalable, reproducible, and user-friendly framework scripted using the ...
raw sequence reads Natural product identification Disease report ABRicate Bowtie 2 FastQC Pandas Snakemake SPAdes Trimmomatic matplotlib numpy scipy pyLabLib Sequence analysis
Free
20
snakemake_chipseq_pe
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Pipeline for the analysis of PE ChIP-seq data
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public

Snakemake pipeline made for reproducible analysis of paired-end Illumina ChIP-seq data. The desired output of this pipelin...
macs2 Bowtie 2 DeepTools fastp SAMtools Snakemake Trimmomatic
Free
21
phytopipe
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Plant Pathogen Detection Pipeline (PhytoPipe) for RNA-seq Data
public

public

# PhytoPipe: A Phytosanitary Pipeline for plant pathogen detection and diagnosis using RNA-seq data PhytoPipe is an open-sour...
RNA sequence Sequence read processing Sequence report bwakit crass Bowtie 2 BWA cloudSPAdes metaspades MultiQC MUMmer4 plasmidspades QUAST rnaspades RVDB-prot seqtk Snakemake SPAdes Trimmomatic Plant biology RNA-Seq
Free
1
viralmetagenomicspipeline
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Pipeline for metagenomic community analysis using DNA isolated from virus-like particles
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public

This repo can be used to generate all of the desired output files for community analysis (shared OTUs, taxonomies, alpha/beta...
r-virfinder bam_to_sam_parallel BBMap BCFtools bcf-tools-cat bcf-tools-index Bowtie 2 BWA-SW CAT and BAT cloudSPAdes mbwa_wrapper metaspades plasmidspades QUAST rnaspades sam_to_bam SAMtools samtools_flagstat samtools_idxstats samtools_slice_bam samtools_sort seqkit Snakemake SPAdes Trimmomatic
Free
45
tosca
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Snakemake workflow for somatic mutation detection without matched normal samples
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public

TOSCA ( T umor O nly S omatic CA lling) is a Snakemake workflow , aimed at performing a somatic varian...
gatk snakemake-wrapper-utils tabix ucsc-bigwigtobedgraph BCFtools bedGraphToBigWig BWA FastQC mosdepth MultiQC Picard SAMtools Snakemake snpEff SnpSift Trimmomatic
Free
61
ccbr_gatk4_exome_seq_pipeline
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An easy-to-use, flexible variant calling pipeline for use on the Biowulf cluster at NIH
public

public

GATK4 Whole Exome-sequencing Pipeline . This is the home of the pipeline, exome-seek. Its long-term goals: to accura...
gatk sequenza-utils BCFtools Bowtie 2 BWA FastQC illumina kraken2 Krona MultiQC Picard QualiMap SAMBLASTER SAMtools Snakemake Trimmomatic VarScan VCFtools MuTect
Free
63