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The Top 23 Bioinformatics Snakemake Open Source Projects

Open source projects categorized as Bioinformatics Snakemake
Categories > Data Processing > Bioinformatics
Categories > Snakemake
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
most recent commit 4 months ago
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.
most recent commit 5 months ago
Snakefmt ⭐ 131
The uncompromising Snakemake code formatter
dependent packages 2total releases 29most recent commit 3 months agopypi snakefmt} Downloads
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))
most recent commit 3 months ago
V Pipe ⭐ 119
V-pipe is a pipeline designed for analysing NGS data of short viral genomes
most recent commit 4 months ago
Smk Simple Slurm ⭐ 80
A simple Snakemake profile for Slurm without --cluster-config
most recent commit a year ago
Tibanna ⭐ 68
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.
dependent packages 1total releases 280most recent commit 3 months agopypi tibanna} Downloads
Panoptes ⭐ 59
Monitor computational workflows in real time
total releases 5most recent commit 4 months ago
Snakefiles ⭐ 58
🐍 Snakefiles for common RNA-seq data analysis workflows.
most recent commit 7 years ago
Sv Callers ⭐ 52
Snakemake-based workflow for detecting structural variants in genomic data
most recent commit a year ago
Dentist ⭐ 44
Close assembly gaps using long-reads at high accuracy.
total releases 13most recent commit 10 months ago
Pipelines.jl ⭐ 39
A lightweight and powerful Julia package for computational pipelines and workflows.
most recent commit 4 months ago
Lsf ⭐ 29
Snakemake profile for running jobs on an LSF cluster
most recent commit 8 months ago
Zarp ⭐ 26
Zavolan-Lab Automated RNA-Seq Pipeline
most recent commit 5 months ago
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.
most recent commit 2 months ago
Phylociraptor ⭐ 23
rapid phylogenomic tree calculator - A highly customizable framework for reproducible phylogenomic inference
most recent commit 5 months ago
Iliad ⭐ 21
ILIAD: A suite of automated Snakemake workflows for processing genomic data for downstream applications
most recent commit 4 months ago
Rna Seq Snakemake ⭐ 20
Snakemake based pipeline for RNA-Seq analysis
most recent commit 5 years ago
Assemblycomparator2 ⭐ 20
🦠📇 Compare prokaryotic genomic assemblies
most recent commit 3 months ago
Pigx_rnaseq ⭐ 19
Pipeline for RNAseq
most recent commit 5 months ago
Kgwasflow ⭐ 19
kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.
most recent commit 6 months ago
Mosaicatcher Pipeline ⭐ 19
Integrated workflow for SV calling from single-cell Strand-seq data
most recent commit 3 months ago
Vesselexpress ⭐ 17
🔬🖥 Automated Blood Vasculature Analysis of 3D Light-Sheet Image Volumes
most recent commit a year ago
The 2 Most Depended On Bioinformatics Snakemake Open Source Projects
The 8 Latest Releases In Bioinformatics Snakemake Open Source Projects
Snakefmt ⭐ 131
The uncompromising Snakemake code formatter
dependent packages 2total releases 29latest release October 05, 2023most recent commit 3 months agopypi snakefmt} Downloads
Panoptes ⭐ 59
Monitor computational workflows in real time
total releases 5latest release August 07, 2023most recent commit 4 months ago
Dentist ⭐ 44
Close assembly gaps using long-reads at high accuracy.
total releases 13latest release September 14, 2022most recent commit 10 months ago
Xebec ⭐ 5
Snakemake pipeline for microbiome diversity effect size benchmarking
total releases 2latest release June 08, 2022most recent commit a year ago
Ymp ⭐ 13
Flexible omics pipeline
total releases 6latest release August 17, 2020most recent commit 3 years ago
Riboraptor ⭐ 9
Tool for ribo-seq analysis
total releases 2latest release April 27, 2018most recent commit 3 years ago
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