All Published Workflows
146 workflows that have been reviewed and published
This Snakemake pipeline implements the GATK best-practices workflow
This Snakemake pipeline implements the GATK best-practices workflow for calling small germline variants. The usage of thi...
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...
A Snakemake workflow to run and benchmark structure learning (a.k.a. causal discovery) algorithms for probabilistic graphical models.
Benchpress [1] is a Snakemake workflow where structure learning algorithms, implemented in possibly different lang...
Amplicon sequence processing workflow using QIIME 2 and Snakemake
Tourmaline is an amplicon sequence processing workflow for Illumina sequence data that uses QIIME 2 and the software pack...
Integrated workflow for SV calling from single-cell Strand-seq data
Structural variant calling from single-cell Strand-seq data Snakemake pipeline. This workflow uses Snakemake to
execu...
mosaicatcher
tabix
BCFtools
BEDTools
ComplexHeatmap
Pandas
pheatmap
SAMtools
Snakemake
TensorFlow
WhatsHap
assertthat
BiocManager
cowplot
data.table
devtools
dplyr
ggnewscale
ggplot2
ggpubr
matrixStats
optparse
RColorBrewer
reshape
reshape2
scales
stringr
tibble
tidyr
intervaltree
matplotlib
numpy
parmap
plotly
pysam
PyYAML
scipy
seaborn
tqdm
xopen
StaG Metagenomic Workflow Collaboration
The StaG Metagenomic Workflow Collaboration (mwc) project focuses on providing
a metagenomics analysis workflow suitable for ...
Cell cycle analysis of single-cell proteomic and transcriptomic data for the FUCCI cell model
This repository contains the code used to perform the single-cell proteogenomic analysis of the human cell cycle . This s...
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
...
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...
Snakemake workflow for comparison of differential abundance ranks
Qadabra is a Snakemake workflow for running and comparing several differential abundance (DA) methods on the same microbiome ...
A repo for the Twist HiFi capture/snakemake workflow
This is a snakemake workflow for analyzing targeted HiFi sequence datasets. The workflow was designed for Twist gene pane...
