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Search results for snakemake

122 search results found

Snakemake ⭐ 2,030

This is the development home of the workflow management system Snakemake. For general information, see

Rna Seq Analysis ⭐ 614

RNAseq analysis notes from Ming Tang

Snakepipes ⭐ 359

Customizable workflows based on snakemake and python for the analysis of NGS data

ATLAS - Three commands to start analyzing your metagenome data

Rna Seq Star Deseq2 ⭐ 282

RNA-seq workflow using STAR and DESeq2

Pypsa Eur ⭐ 278

PyPSA-Eur: A Sector-Coupled Open Optimisation Model of the European Energy System

Sunbeam ⭐ 157

A robust, extensible metagenomics pipeline

Metagem ⭐ 155

💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

Dna Seq Gatk Variant Calling ⭐ 138

This Snakemake pipeline implements the GATK best-practices workflow

Sequana ⭐ 136

Sequana: a set of Snakemake NGS pipelines

Dropseqpipe ⭐ 134

A SingleCell RNASeq pre-processing snakemake workflow

Seq2science ⭐ 132

Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.

Snakefmt ⭐ 131

The uncompromising Snakemake code formatter

Multiprime ⭐ 123

multiPrime is a mismatch-tolerant minimal primer set design tool for large and diverse sequences (e.g. Virus). Here is a web-based version (test: http://multiPrime.cn))

Documentation of the Snakemake-Workflows project

V-pipe is a pipeline designed for analysing NGS data of short viral genomes

Smk Simple Slurm ⭐ 80

A simple Snakemake profile for Slurm without --cluster-config

Dna Seq Varlociraptor ⭐ 76

A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, pedigree, populations) via the unified statistical model of Varlociraptor.

Grenepipe ⭐ 75

A flexible, scalable, and reproducible pipeline to automate variant calling from sequence reads.

Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.

Rna Seq Kallisto Sleuth ⭐ 63

A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.

Panoptes ⭐ 59

Monitor computational workflows in real time

Snakefiles ⭐ 58

🐍 Snakefiles for common RNA-seq data analysis workflows.

Snakecharm ⭐ 58

Plugin for PyCharm / IntelliJ IDEA Platform IDEs which adds support for Snakemake language.

Pyflow Chipseq ⭐ 55

a snakemake pipeline to process ChIP-seq files from GEO or in-house

Pytest Workflow ⭐ 52

Configure workflow/pipeline tests using yaml files.

Sv Callers ⭐ 52

Snakemake-based workflow for detecting structural variants in genomic data

Close assembly gaps using long-reads at high accuracy.

Pipelines.jl ⭐ 39

A lightweight and powerful Julia package for computational pipelines and workflows.

Pyflow Atacseq ⭐ 37

ATAC-seq snakemake pipeline

Hecatomb ⭐ 36

hecatomb is a virome analysis pipeline for analysis of Illumina sequence data

Snakemake Econ R ⭐ 35

reproducible research project template for R using Renv and snakemake with an econ application

Tourmaline ⭐ 32

Amplicon sequence processing workflow using QIIME 2 and Snakemake

Snakemake Mode ⭐ 32

[MIRROR] Emacs support for Snakemake

Ngs_pipeline ⭐ 31

Exome/Capture/RNASeq Pipeline Implementation using snakemake

Pubrunner ⭐ 29

A framework for keeping biomedical text mining result up-to-date

Snakemake profile for running jobs on an LSF cluster

Zavolan-Lab Automated RNA-Seq Pipeline

Technology-invariant pipeline for spatial-omics analysis (Xenium / MERSCOPE / CosMx / PhenoCycler / MACSima / Hyperion) that scales to millions of cells

Atacseq_pipeline ⭐ 25

Ultimate ATAC-seq Data Processing & Quantification Workflow. A Snakemake implementation of the BSF's ATAC-seq Data Processing Pipeline extended by downstream quantification and annotation steps using bash and Python.

mapping pipeline for ancient DNA

Phylociraptor ⭐ 23

rapid phylogenomic tree calculator - A highly customizable framework for reproducible phylogenomic inference

Explore the impacts of 24/7 Carbon-Free Energy PPAs

ILIAD: A suite of automated Snakemake workflows for processing genomic data for downstream applications

Assemblycomparator2 ⭐ 20

🦠📇 Compare prokaryotic genomic assemblies

Snek5000 ⭐ 20

🐍 Python framework for Nek5000 🚀

Rna Seq Snakemake ⭐ 20

Snakemake based pipeline for RNA-Seq analysis

Use an ensemble of variant callers to call variants from ATAC-seq data

snakemake pipeline for Hi-C post-processing

Mosaicatcher Pipeline ⭐ 19

Integrated workflow for SV calling from single-cell Strand-seq data

Pigx_rnaseq ⭐ 19

Pipeline for RNAseq

Kgwasflow ⭐ 19

kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.

Metameta ⭐ 18

Tailseeker ⭐ 18

Software for measuring poly(A) tail length and 3′-end modifications using a high-throughput sequencer

Vesselexpress ⭐ 17

🔬🖥 Automated Blood Vasculature Analysis of 3D Light-Sheet Image Volumes

Rna Seq Pop ⭐ 17

Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data

Cookiecutter Reproducible Research ⭐ 16

A cookiecutter template for reproducible research projects using Python, Snakemake, and Pandoc.

Snakemake skeleton - Build workflows with Snakemake

A NGS analysis framework for WGS data, which automates the entire process of spinning up AWS EC2 spot instances and processing FASTQ to snvVCF in <60m, for dollars a sample and achieving Fscores of 0.998.

Pyflow Rnaseq ⭐ 15

RNAseq pipeline based on snakemake

Pipelines in genomics

Snakemake Novice Bioinformatics ⭐ 14

Introduction to Snakemake for Bioinformatics

Snakebids ⭐ 14

Snakemake + BIDS

Snakemake Wrappers ⭐ 14

🐍 Snakemake wrappers for bioinformatics.

Ngs Test Data ⭐ 14

A workflow for creating small NGS test data sets, useful for continuous integration.

Nbpipeline ⭐ 14

Snakemake-like pipeline manager for reproducible Jupyter Notebooks

Snakemake workflow for comparison of differential abundance ranks

Flexible omics pipeline

Transflow ⭐ 12

A snakemake workflow for WGS-based tuberculosis transmission analysis

Ngs Pipeline ⭐ 12

Pipeline for Somatic Variant Calling with WES and WGS data

Genome Seek ⭐ 12

Clinical Whole Genome Sequencing Pipeline

Mikropml Snakemake Workflow ⭐ 12

Snakemake template for building reusable and scalable machine learning pipelines with mikropml

Get a nicely-chunked local copy of the biomedical literature (to use for other projects)!

Catd_snakemake ⭐ 11

Snakemake pipeline for benchmarking cell-type deconvolution methods as well as deconvoluting real bulk RNA-seq data with the use of scRNA-seq datasets

2019_embl Abr_snakemake_webinar ⭐ 11

Scripts and Snakemake pipeline used in the EMBL-ABR webinar

Enrichment_analysis ⭐ 10

A Snakemake workflow for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, and GSEApy.

Preprocessing pipeline for (sc)ATAC data

Cascabel ⭐ 10

Automated pipeline for amplicon sequence analysis

Snakemake based framework for NGS data analysis and management

Pigx_bsseq ⭐ 10

bisulfite sequencing pipeline from fastq to methylation reports

Phylogenetic Placement Evaluation Workflows : Benchmark placement software and different reference trees

Solar And Wind Potentials ⭐ 10

Estimation of solar and wind power generation potentials in Europe.

MONSDA, Modular Organizer of Nextflow and Snakemake driven hts Data Analysis

A Sphinx extension for Snakemake workflows

Riboraptor ⭐ 9

Tool for ribo-seq analysis

Triti Map ⭐ 9

A Snakemake-based pipeline for gene mapping in Triticeae.

💻💻💻 A commandline tool for analysis of big biological data sets for distributed HPC clusters.

Unsupervised_analysis ⭐ 9

A general purpose Snakemake workflow to perform unsupervised analyses (dimensionality reduction & cluster analysis) and visualizations of high-dimensional data.

cwl/wdl/sm/nf files, tool and workflow metadata, and input specifications.

Project Diploid Assembly ⭐ 8

Pipeline code for creating a fully haplotype-resolved assembly from a combination of PacBio/ONT long reads and Illumina Strand-seq data

We present HRIBO (High-throughput annotation by Ribo-seq), a workflow to enable reproducible and high-throughput analysis of bacterial Ribo-seq data. The workflow performs all required pre-processing steps and quality control. Importantly, HRIBO outputs annotation-independent ORF predictions based on two complementary prokaryotic-focused tools, and integrates them with additional computed features. This facilitates both the rapid discovery of ORFs and their prioritization for functional charact

Snakemake_rnaseq ⭐ 8

A Snakemake pipeline to go from fastq mRNA sequencing files to raw and normalised counts (usable for downstream EDA and differential analysis)

Multiple_sclerosis_proj ⭐ 8

Data analysis platform/structure, machine learning/AI project for multiple sclerosis

zAMP is a bioinformatic pipeline designed for convenient, reproducible and scalable amplicon-based metagenomics

A pipeline to use Lep-Map3 to create linkage maps and LepAnchor for anchoring and orienting genome assemblies with said linkage maps.

Snakemake Workflow Fermi Lat ⭐ 7

A Snakemake workflow for Fermi-LAT data reduction

Simulation Comparison ⭐ 7

Snakemake workflow to benchmark scRNA-seq data simulators

Lescroart2023 ⭐ 7

Archived code for analyses in "Extensive phylogenomic discordance and the complex evolutionary history of the Neotropical cat genus Leopardus" (Lescroart et al. 2023, MBE)

🗺️ MAPP is a computational method which enables identification of binding motifs for RNA-binding proteins that shape pre-mRNA processing under specific conditions.

JAMIRA is a reproducible Workflow for Integrative Exploration of Genomic Features of prokariotes

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