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awesome-bacteria

List of computational resources for analyzing bacterial sequencing data.
https://github.com/alexeyrakov/awesome-bacteria

Last synced: 3 days ago
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Software packages
- GWAS
  - treeWAS - [R] - A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes.
  - SEER - [C++] - Sequence element (kmer) enrichment analysis.
  - bugwas - [R] - Locus and lineage tests for bacterial GWAS.
  - DBGWAS - [C++] - A tool for quick and efficient bacterial GWAS.
  - bacterialGWAS - [R] - A pipeline for performing genome-wide association tests for bacterial genomes.
  - bacterial_GWAS_tutorial - [R] - Tutorial for bacterial GWAS pipline and bugwas, created for Bodega Bay 2016 NGS workshop.
  - Scoary - [Python] - Microbial pan-genome wide association studies.
  - Roary - [Perl] - Rapid large-scale prokaryote pan genome analysis.
- Bacterial population genomics
  - bac-genomics-scripts - [Perl] - Collection of scripts for bacterial genomics.
  - PuppetMaster - [Python] - Variable sites extractor.
  - snp-sites - [C] - Rapid efficient extractor of SNPs from multi-FASTA alignments.
- Other applications
  - poppr - [R] - An R package for genetic analysis of populations with mixed (clonal/sexual) reproduction.
Tutorials and workflows
- Other applications
  - scientific_python_cheat_sheet - Scientific Python Cheat Sheet.
Educational resources
- Other applications
  - CSHL Programming for Biology 2019 - CSHL Programming for Biology course official site (2019).
  - CSHL Programming for Biology - CSHL Programming for Biology (2019), all lectures and scripts.
  - CSHL Programming for Biology - CSHL Programming for Biology (2012), all lectures and scripts.
  - CSHL NGS - DNA analysis for the CSHL Programming for Biology course (2012-2014).
  - GEN220_2020 - GEN220: High Throughput Biological Data Analysis (2020).
  - GEN220 2015 - Computational Analysis of High Throughput Biological Data (2015).
  - programming-intro - Computational Analysis of High Throughput Biological Data (2018).
  - BCB546X-Spring2022 - Computational Skills for Biological Data (Spring 2022).
  - BCB546X-Fall2017 - Computational Skills for Biological Data (Fall 2017).
  - Introduction - Talks and Materials for "An Introduction to Bioinformatics".
  - Course-Programme - Course in Working with bacterial communities and populations (2016).
  - 2016-05-16-CAM - Data Carpentry (2016).
  - experimental-design - Experimental Design.
  - winter-school2016 - Essential Data Analysis Skills for Biologists (2016).
  - functional-genomics-workshop-orange - Data Mining w/o Programming Workshop (2014).
  - Data Analysis for the Life Sciences - Data Analysis for the Life Sciences (2015): Biomedical Data Science, Introduction to Bioconductor: Annotation and analysis, High-performance computing for reproducible genomics with Bioconductor.
  - microbial-informatics-2014 - Microbial Informatics 2014 Labs.
  - In-depth-NGS-Data-Analysis-Course - In-depth NGS Data Analysis Course (2018).
  - CSHL Programming for Biology 2019 - CSHL Programming for Biology course official site (2019).
  - Molecular Phylogenetics - Molecular Phylogenetics Course (2017).
- Shell
  - shell-novice - Software Carpentry introduction to the shell for novices (2017).
  - shell-extras - Software Carpentry Extra Unix Shell Material (2017).
  - shell-genomics - Data Carpentry Shell Genomics lessons (2017).
- Python
  - 2015-python-intro - An Introduction to Python (2015).
  - 2016-adv-begin-python - Advanced Beginner Python (2016).
  - python-beginners - Introduction to programming with Python (2015) (incl. Russian).
  - python-novice-gapminder - Software Carpentry Plotting and Programming in Python (2017).
  - python-novice-inflammation
  - python-data-intro - Introduction to Data Processing with Python (2015).
  - BPBR16 - Bioinformatics using Python for Biomedical Researchers (2016).
  - 2017-python-programming - Programming with Python (2017).
  - evop2018 - Programming for Evolutionary Biology Python in 2 Days (2018).
  - Py4Bio - Public data for the book Python for Bioinformatics.
- R & RStudio
  - r-novice-gapminder - Software Carpentry R for Reproducible Scientific Analysis (2017).
  - r-novice-inflammation - Software Carpentry introduction to R for novices using inflammation data (2017).
  - r-intro - Cambridge Basic R Course (2017).
  - r-intermediate - Data Manipulation and Visualisation using R (Intermediate R Course).
  - R-Data-Skills - R for Reproducible Scientific Analysis (2016).
  - R-genomics - Data Carpentry Data Analysis and Visualization in R (2017).
  - webinars - Code and slides for RStudio webinars.
- Galaxy
  - galaxy-intro - Introduction to Galaxy: data manipulation and visualisation course (2017).
  - training-material - A collection of Galaxy-related training material.
- Bioconductor
  - ngs-in-bioc - A course on Analysing NGS data using Bioconductor (2015).
  - BiocIntro - Bioconductor introduction (2017).
  - BioC2016Introduction - Bioconductor introduction (2016).
  - LearnBioconductor - Learning R / Bioconductor for Sequence Analysis (2015).
  - UseBioconductor - Use R / Bioconductor for Sequence Analysis (2015).
  - useR2015 - Course material for useR 2015 workshop -- Bioconductor for High Throughput Sequence Analysis (2015).
  - BioC2015Introduction - Introduction to R and Bioconductor (2015).
  - BiocUruguay2015 - R Bio: Untangling Genomes (2015).
  - BiocEMBO2015 - EMBO Practical Course: Analysis of High-Throughput Sequencing Data (2015).
  - CSAMA2015 - CSAMA 2015: Statistics and Computing in Genome Data Science (2015).
- Git
  - git-novice - Software Carpentry Version Control with Git (2017).
- Docker
  - docker-4-bioinformatics - Introduction to Docker for Bioinformatics (2017).
Web portals and apps
- Other applications
  - Sofware Carpentry

Programming Languages

HTML 13 R 12 Python 11 Shell 4 Perl 3 Jupyter Notebook 2 JavaScript 2 TeX 1 CSS 1 PostScript 1

Ecosyste.ms: Awesome

awesome-bacteria

Software packages

GWAS

Bacterial population genomics

Other applications

Tutorials and workflows

Other applications

Educational resources

Other applications

Shell

Python

R & RStudio

Galaxy

Bioconductor

Git

Docker

Web portals and apps

Other applications