All Published Workflows
132 workflows that have been reviewed and published
![atlas](https://media.bioworkflows.com/bioworkflows/public_preview/2e9488df62bdb57adbd8f8a137263f57f970f5571566588f6242d63f73c67151.jpg)
ATLAS - Three commands to start analyzing your metagenome data
Metagenome-atlas is a easy-to-use metagenomic pipeline based on snakemake. It handles all steps from QC, Assembly, Binning, t...
raw sequence reads
Genome assembly
Annotation track
checkm2
gunc
prodigal
snakemake-wrapper-utils
MEGAHIT
Atlas
BBMap
Biopython
BioRuby
Bwa-mem2
cd-hit
CheckM
DAS
Diamond
eggNOG-mapper v2
MetaBAT 2
Minimap2
MMseqs
MultiQC
Pandas
Picard
pyfastx
SAMtools
SemiBin
Snakemake
SPAdes
SqueezeMeta
TADpole
VAMB
CONCOCT
ete3
gtdbtk
h5py
networkx
numpy
plotly
psutil
utils
metagenomics
![pipeline-transcriptome-de](https://media.bioworkflows.com/bioworkflows/public_preview/602f5af232359582918564dd5a4f011be7be53b91e1b71369ede3cf7221c6120.jpg)
Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
This project is deprecated. Please see our newer wf-transcriptomes , which contains functionality for differential exp...
![nanopype](https://media.bioworkflows.com/bioworkflows/public_preview/b2f9dc40c9203873de837f121f13d61ff30419fdd659eb62f656ca95188a11c9.jpg)
Snakemake pipelines for nanopore sequencing data archiving and processing
Detailed documentation and tutorials are available at readthedocs . Nanopype is a snakemake based pipeline providing conv...
![stainedglass](https://media.bioworkflows.com/bioworkflows/public_preview/806d018c3cb232f52b73e59ded90b880e1dde535430b4937b7c55abda2eade05.jpg)
Make colorful identity heatmaps of genomic sequence
This is a repository for making colorful identity heatmaps of genomic sequence. To install you can follow the directions on t...
![lathe](https://media.bioworkflows.com/bioworkflows/public_preview/1f180f3eaf10aa1f49825688bd4634606b3e4c92a2d6c655dd34486bf7715039.jpg)
A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
A tool for generating bacterial genomes from metagenomes with Nanopore long read sequencing First, install miniconda3 The...
![assembly-annotation-pipeline](https://media.bioworkflows.com/bioworkflows/public_preview/183a4cb292c47778ccbe1f01eb4b0b18af2148d783cb2b0a7a6d32cf4ac5b3f3.jpg)
Plant genome assembly and annotation pipeline using snakemake
This Snakemake pipeline aims for plant genome assembly with HiFi data and genome annotation with RNA-Seq/IsoSeq. Modified fro...
![score-assemblies](https://media.bioworkflows.com/bioworkflows/public_preview/d00200dfb7483e04ff9df2ae8ccf321113edce92a30cf20ff777932747cc26f1.jpg)
Score and compare multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s)
A snakemake-wrapper for evaluating de novo bacterial genome assemblies, e.g. from Oxford Nanopore (ONT) or Illumina seque...
![uncovar](https://media.bioworkflows.com/bioworkflows/public_preview/81f9768cc8e6e96ca0b24ce2ae4ce244b89d0d4e8b1a84b7a7a33388e8e7b0ae.jpg)
Transparent and robust SARS-CoV-2 variant calling and lineage assignment with comprehensive reporting.
A reproducible and scalable workflow for transparent and robust SARS-CoV-2
variant calling and lineage assignment with com...
JSON
raw sequence reads
Variant calling
genetic variants
delly
nanofilt
rust-bio-tools
snakemake-wrapper-utils
tabix
BCFtools
Biopython
BWA
CANU
Consensus
fastp
FastQC
fgbio
FreeBayes
GFFutils
kallisto
Kraken
Krona
Medaka
metaspades
Minimap2
MultiQC
Pandas
Pangolin
Picard
Quant
QUAST
SAMtools
Snakemake
Variant Effect Predictor (VEP)
vembrane
altair
intervaltree
numpy
pysam
requests
Varlociraptor
COVID19 Risk Mitigation
![single-cell-nanopore](https://media.bioworkflows.com/bioworkflows/public_preview/1fc87665f143126cfbe730f9baae6e0a413dc8fb9637bd6be4acfaae6c23668c.jpg)
Workflow for Nanopore Sequencing of 10x single cell libraries
ScNapBar (single-cell Nanopore barcode demultiplexer) is a workflow to assign barcodes to long-read single-cell sequencing...
![ont-assembly-snake](https://media.bioworkflows.com/bioworkflows/public_preview/614924dd3909209ac896d3af3d2cd3441df9d7b032ab9bd7bf06f302a262628b.jpg)
Snakemake workflow for bacterial genome assembly + polishing for Oxford Nanopore (ONT) sequencing using multiple tools
A snakemake-wrapper for easily creating de novo bacterial genome assemblies from Oxford Nanopore (ONT) sequencing data, a...
![kgwasflow](https://media.bioworkflows.com/bioworkflows/public_preview/5cc254ffe644790f627a57524b722e3a617b82dd61ffd3994e6a961b954f0b58.jpg)
kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.
A modular, flexible, and reproducible Snakemake workflow to perform k-mers-based GWAS.
Summary
Installation
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![lathe](https://media.bioworkflows.com/bioworkflows/public_preview/357c264c395fb6e0f67eabd9d0627d86c23a923a76ea26ed3a2e88874a204cb4.jpg)
A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
A tool for generating bacterial genomes from metagenomes with Nanopore long read sequencing First, install miniconda3 The...