Top 11 Python Snakemake Projects

• RNA-seq-analysis

  1 809 0.0 Python

  RNAseq analysis notes from Ming Tang

• atlas

  2 346 9.3 Python

  ATLAS - Three commands to start analyzing your metagenome data (by metagenome-atlas)

  

• WorkOS

  workos.com sponsored

  The modern identity platform for B2B SaaS. The APIs are flexible and easy-to-use, supporting authentication, user identity, and complex enterprise features like SSO and SCIM provisioning.

  

• pypsa-eur

  3 284 9.9 Python

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

  

• metaGEM

  14 165 6.3 Python

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

Project mention: Metagenomic samples analysis: From taxonomic classification to reads mapping | /r/bioinformatics | 2023-06-09

Maybe this workflow will be interesting to you: it assembles metagenomes, generates bins, and also creates metabolic models for predicting interactions within microbiomes 💎 https://github.com/franciscozorrilla/metaGEM

• sv-callers

  1 70 2.9 Python

  Snakemake-based workflow for detecting structural variants in genomic data

  

• rna-seq-kallisto-sleuth

  1 63 5.9 Python

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

  

• cookiecutter-snakemake-workflow

  1 55 1.8 Python

  A cookiecutter template for Snakemake workflows

  

• InfluxDB

  www.influxdata.com sponsored

  Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.

  

• hecatomb

  1 41 8.5 Python

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

Project mention: Viral Metagenomics - assembly/annotation issues | /r/bioinformatics | 2023-05-23

Try this https://github.com/shandley/hecatomb

• zarp

  1 28 7.2 Python

  The Zavolab Automated RNA-seq Pipeline (by zavolanlab)

  

Project mention: Any links to R-scripts for common NGS pipelines? | /r/bioinformatics | 2023-05-11

• GermlineMutationCalling

  1 12 0.0 Python

  An adaptable Snakemake workflow which uses GATKs best practice recommendations to perform germline mutation calling starting with BAM files

• chipseq-smk-pipeline

  2 3 7.3 Python

  ChIP-Seq processing pipeline on snakemake

  

Python Snakemake related posts

• Metagenomic samples analysis: From taxonomic classification to reads mapping
  1 project | /r/bioinformatics | 9 Jun 2023
• Is Developing a Multi-omics Pipeline Feasable for a Masters Thesis?
  1 project | /r/bioinformatics | 19 May 2023
• MetaQuast for assembling samples from complex communities
  1 project | /r/bioinformatics | 27 Jul 2022
• Finding BGCs from antiSMASH database in metagenomes
  1 project | /r/bioinformatics | 21 Jul 2022
• Need guidance/plan/roadmap to transition from bioinformatics to systems biology and netwrok biology.
  1 project | /r/bioinformatics | 15 Jul 2022
• U.S. can get to 100% clean energy with wind, water, solar and zero nuclear, Stanford professor says
  1 project | /r/environment | 7 Mar 2022
• Looking for Voluntary/Part-time Bioinformatics projects/work!!
  1 project | /r/bioinformatics | 26 Nov 2021
• A note from our sponsor - WorkOS
  workos.com | 30 Apr 2024

  The APIs are flexible and easy-to-use, supporting authentication, user identity, and complex enterprise features like SSO and SCIM provisioning. Learn more →

Index

Sponsored

SaaSHub - Software Alternatives and Reviews

SaaSHub helps you find the best software and product alternatives

www.saashub.com

Do not miss the trending Python projects with our weekly report!