All Published Workflows
81 workflows that have been reviewed and published
![kraken2_classification](https://media.bioworkflows.com/bioworkflows/public_preview/7a6a1fc5df6f57a31b800266881003949ffd206a1fb736004fc09825dfc9ba7d.jpg)
Snakemake workflow for metagenomic classification with Kraken2
A Snakemake pipeline wrapper of the Kraken2 short read metagenomic classification software, with additional tools for analysi...
![struo](https://media.bioworkflows.com/bioworkflows/public_preview/6c95e47da040bdda2c59dbe9d06ef7d56afa700e826eb6ef10599a14a19093e8.jpg)
![phanta](https://media.bioworkflows.com/bioworkflows/public_preview/60692bead9908136ac0585a7289753a9ce303a8e989c51d923fca58fa9948924.jpg)
Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes
Workflow figure created on BioRender.com. Pinto, Y., Chakraborty, M., Jain, N. et al. Phage-inclusive profiling of human gut ...
![covid-19-signal](https://media.bioworkflows.com/bioworkflows/public_preview/654963db437af051ec1197e3ab2a3eb4c6cbdc09928cdc2b32ea2aa3d58d2787.jpg)
Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.
This is a complete standardized workflow the assembly and subsequent analysis for short-read viral sequencing.
This core work...
![stag-mwc](https://media.bioworkflows.com/bioworkflows/public_preview/d1aa95ef58e060110d23438f69ce196d8016620c23b2a73a1b07b340a634f0b0.jpg)
StaG Metagenomic Workflow Collaboration
The StaG Metagenomic Workflow Collaboration (mwc) project focuses on providing
a metagenomics analysis workflow suitable for ...
![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...
![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
![rna-seek](https://media.bioworkflows.com/bioworkflows/public_preview/ca6935df19a668d21a38d87bdc51235db68095494893cb02f0fcc8a102021fbd.jpg)
![ccbr_gatk4_exome_seq_pipeline](https://media.bioworkflows.com/bioworkflows/public_preview/fe92fb021bda9de96be5de3eb061ee06e7a73228d3399cc158ccf16672c5f7dc.jpg)
An easy-to-use, flexible variant calling pipeline for use on the Biowulf cluster at NIH
GATK4 Whole Exome-sequencing Pipeline
. This is the home of the pipeline, exome-seek. Its long-term goals: to accura...
![pipelord](https://media.bioworkflows.com/bioworkflows/public_preview/3009b7d6f285d3a77010868cf5ad377c07fe537b9084c4a6ab79a2d928df3e59.jpg)
A microbial genomic analysis pipeline used by the Djordjevic Lab
This repo contains a genomic analysis pipeline used for analysing mostly E. coli genomes, though it also sees use in anal...
![on-rep-seq](https://media.bioworkflows.com/bioworkflows/public_preview/5062837b596a31f9603b50e6c4b67ed25e3001ad907aa133a269ba77b33e230c.jpg)
Bulk Typing of Bacterial Species down to Strain Level
ON-rep-seq is a molecular method where bacterial (or yeast) selective intragenomic fragments generated with Rep-PCR are seque...
![methyl-seek](https://media.bioworkflows.com/bioworkflows/public_preview/5c49cdfbe5de7c9ccd4d22352584c076e65eb76018fe3ee1c1aaed2b7af4cf38.jpg)