A DRAFT, early stage book on snakemake.
☆25Nov 1, 2023Updated 2 years ago
Alternatives and similar repositories for 2023-snakemake-book-draft
Users that are interested in 2023-snakemake-book-draft are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- A toolkit for quality control & adjustment of nucleotide redundancy in bacterial pan-genome analyses☆21Feb 12, 2026Updated 7 months ago
- Code for the paper "Learning the fitness dynamics of pathogens from phylogenies"☆26Feb 26, 2026Updated 6 months ago
- An R Markdown template using the bookdown package for preparing a PhD thesis at the University of California Davis☆16Dec 6, 2023Updated 2 years ago
- Neptune: Genomic Signature Discovery☆22May 1, 2026Updated 4 months ago
- The PanGenome Graph Builder☆17Jul 17, 2024Updated 2 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- notes on the farm cluster☆16Feb 26, 2025Updated last year
- Cookiecutter profile for making a Snakemake-based bioinformatics tool, but without the fluff☆51Oct 17, 2023Updated 2 years ago
- Resolving Species Level Classification Using Emu☆14Jun 14, 2024Updated 2 years ago
- Nextflow pipeline designed for rapid onsite QC and variant calling of Oxford Nanopore data (following basecalling and demultiplexing with…☆13Jun 4, 2026Updated 3 months ago
- AMR/VF LGT focused bacterial genomics analysis workflow☆28Feb 19, 2026Updated 7 months ago
- Analysing the genomic context of mobile genes☆11Jul 21, 2025Updated last year
- Metagenomic pipeline managed by snakemake☆18Sep 18, 2024Updated 2 years ago
- tool to determine optimal refrerence genome given a set of fasta files☆15May 18, 2023Updated 3 years ago
- Variant calling pipeline designed for Q20+ ONT long-reads☆15Sep 14, 2026Updated last week
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Scripts and reference files to type Group A Streptococcus☆11Aug 31, 2026Updated 3 weeks ago
- Inferring spatiotemporal dynamics of H5N1 influenza from sequence data☆10Sep 6, 2013Updated 13 years ago
- Materials for the STAMPS 2024 course at the MBL in Woods Hole, MA, USA☆13Jul 25, 2024Updated 2 years ago
- Omics data analysis☆17Feb 25, 2026Updated 6 months ago
- Functional Flow Calculator☆14Oct 11, 2024Updated last year
- A package for making tree-based visualizations for embedding vectors☆10Feb 6, 2023Updated 3 years ago
- Identify and remove contaminants from metagenome-assembled genomes☆18Feb 16, 2024Updated 2 years ago
- An R client for the online Functional Flows Calculator API☆11Mar 23, 2023Updated 3 years ago
- Run a command and report its process tree's CPU, memory, and I/O usage☆21Updated this week
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- High throughput python tool for mining and analysis of gene duplications.☆17Jul 30, 2026Updated last month
- TAXnomic Profile Aggregation and STAndardisation☆45May 2, 2026Updated 4 months ago
- Simple-to-use interactive comparison of two bacterial genomes☆28Jan 30, 2026Updated 7 months ago
- Snakemake workflow management system and CLI generation tool☆67Oct 22, 2025Updated 11 months ago
- Correcting errors in noisy long reads using variation graphs☆53Nov 17, 2022Updated 3 years ago
- ☆13Sep 1, 2020Updated 6 years ago
- A template for a Markdown/Pandoc template for a UC Davis PhD dissertation or Masters' thesis☆23Feb 20, 2016Updated 10 years ago
- Example repository to show how to build and deploy jupyterlite with pixi☆18Jul 30, 2024Updated 2 years ago
- A filter algorithm with program to filter an alignment or mapping file☆12May 15, 2025Updated last year
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- ☆14Sep 11, 2026Updated last week
- Plasmid analysis using rearrangement distances☆56Jul 19, 2026Updated 2 months ago
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆50Feb 20, 2026Updated 7 months ago
- AI-powered Documentation and Test Generation Tool☆119Aug 1, 2026Updated last month
- Simulate mutations in genomes☆15Jun 15, 2020Updated 6 years ago
- Fast pairwise transmission inference from single genome and/or metagenomic data☆39Aug 21, 2026Updated last month
- emm Automatic Isolate Labeller☆16Mar 25, 2025Updated last year