All Published Workflows
110 workflows that have been reviewed and published
![natrix](https://media.bioworkflows.com/bioworkflows/public_preview/e869c6522fdc626f4352051ec23940335655df117c2d7043aaa2d8b10f40a115.jpg)
Open-source bioinformatics pipeline for the preprocessing of raw sequencing data.
Natrix is an open-source bioinformatics pipeline for the preprocessing of raw sequencing data.
The need for a scalable, repro...
![mapache](https://media.bioworkflows.com/bioworkflows/public_preview/bb656e17ac94b23426305db1b39bff6177b185cdd574346d96093c6f5281264c.jpg)
mapping pipeline for ancient DNA
Mapache ([maˈpa.t͡ʃe]) is a lightweight mapping pipeline for ancient DNA using the workflow manager Snakemake . Visit ...
![metax_bakeoff_2019](https://media.bioworkflows.com/bioworkflows/public_preview/48401497a40c435096f2c8dd457320a4966c9b360c6802c0abd714c0f999e8ef.jpg)
Metagenomic Taxonomic Classification Benchmarking Workflow
Metagenomic taxonomic classification benchmarking This package is contains snakemake workflows, a jupyter notebook and a pyth...
![mof-search](https://media.bioworkflows.com/bioworkflows/public_preview/60257784e62dd17304ec9c7deb5084bb8e395c22c9cf0e91b74e536e0769836e.jpg)
BLAST-like search across all pre-2019 bacteria on ordinary laptop and desktop computers within a few hours
Introduction
Citation
Installation
Step 1: Install dependencies
Step 2: Clone the re...
![kount](https://media.bioworkflows.com/bioworkflows/public_preview/2262df808815e8f0a8cc19bedd5dca8d7b735f34acdac6369a4240b8f78dde3b.jpg)
Snakemake pipeline calculating KEGG orthologue abundance in metagenomic sequence data.
Snakemake pipeline calculating KEGG orthologue abundance in metagenomic sequence data. KOunt is a Snakemake pipeline that cal...
![oecophylla](https://media.bioworkflows.com/bioworkflows/public_preview/a6c58d38076f5b7588be5c85489f5705eb2f396621306c8a054aa6cef1d7bba9.jpg)
Modular Shotgun Sequence Analysis Workflow: Oecophylla - Harnessing Snakemake
Canonically pronounced ee-co-fill-uh , Oecophylla is a Snakemake wrapper for shotgun sequence analysis. Rather than being...
![nbis-meta](https://media.bioworkflows.com/bioworkflows/public_preview/a313d869a5ece3cb72c146dd91f5ddf1cba1017dc12325245ea497335fce687c.jpg)
A snakemake workflow for metagenomic projects
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
![ameta](https://media.bioworkflows.com/bioworkflows/public_preview/69dd01137d0ae012a95788d05e91437b4d97f42b53a32a7ca5c8098cebd5dedf.jpg)
![mag_snakemake_wf](https://media.bioworkflows.com/bioworkflows/public_preview/7bb19139c8b1750049fa4c4888ddb2f4ed3444d77957d60fd761282e6ad60aef.jpg)
Recovery of prokaryotic genomes from shotgun metagenomic sequencing data
Overview
System Requirements
Workflow setup
Running pipeline
CPU time
License
...
![pacman-pipeline](https://media.bioworkflows.com/bioworkflows/public_preview/c0d52259b3a96514e06006619903f013a8f42cc264249e87a7b8fe9beb1a65a3.jpg)
Bioinformatics pipeline for the analysis of amplicon sequencing data of eDNA samples from the PacMAN project
This is the bioinformatics pipeline developed for the PacMAN (Pacific Islands Marine Bioinvasions Alert Network). This pipeli...
![gavisunk](https://media.bioworkflows.com/bioworkflows/public_preview/6e687279fab64383a30f6110f0389fda9664ff92674576ffa93246c6447eba9d.jpg)
Genome Assembly Validation via Inter-SUNK distances in ONT reads
Genome Assembly Validation via Inter-SUNK distances in nanopore reads Setup source files in config.yaml and ont.tsv config.ya...
![phytopipe](https://media.bioworkflows.com/bioworkflows/public_preview/8c20d707da359d08214d193629dcf71e6d6f2e5be814d0425e8602a5392d92c5.jpg)
Plant Pathogen Detection Pipeline (PhytoPipe) for RNA-seq Data
# PhytoPipe: A Phytosanitary Pipeline for plant pathogen detection and diagnosis using RNA-seq data PhytoPipe is an open-sour...