Run shell commands in a scientifically reproducible and robust way
☆34Sep 11, 2026Updated last month
Alternatives and similar repositories for scicommander
Users that are interested in scicommander are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Chimera: A Versatile Metagenomic Classification Tool☆21Updated this week
- Optimal distance lower bound k-mer sampling.☆12Jun 19, 2024Updated 2 years ago
- Benchmarking different ways of doing read (taxonomic) classification, with a focus on removal of contamination and MTB classification☆14Apr 8, 2024Updated 2 years ago
- Visualize microbial evolution at the SNP level!☆18Aug 12, 2025Updated last year
- Fast and space-efficient taxonomic classification of long reads☆46Jul 16, 2026Updated 2 months ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Website and slides for intro to bioinformatics class at Fred Hutch☆13Jun 4, 2018Updated 8 years ago
- A Slack bot for LLM/ImageGen responses using an OpenAI API backend (LlamaCPP, Ollama, etc)☆14Updated this week
- ProphAsm – a rapid computation of simplitigs directly from k-mer sets☆25Feb 17, 2023Updated 3 years ago
- mGEMS Genomic epidemiology with mixed samples☆17Sep 4, 2024Updated 2 years ago
- Ultra-rapid detection of viral variants directly from sequencing data☆48Sep 16, 2026Updated 3 weeks ago
- Factorize metagenotypes to infer strains and their abundances☆12Sep 29, 2024Updated 2 years ago
- A nextflow pipeline for performing bacterial RNA-Seq data analysis☆15Sep 25, 2026Updated 2 weeks ago
- ☆30Mar 6, 2025Updated last year
- Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]☆49Jun 19, 2026Updated 3 months 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.
- Overview of our data for microbial genomic benchmarking☆41Jun 19, 2026Updated 3 months ago
- Plasmid analysis using rearrangement distances☆56Jul 19, 2026Updated 2 months ago
- Nail is an Alignment Inference tooL☆71Sep 29, 2026Updated 2 weeks ago
- Phylogenetic Likelihood Library 2 - experimental☆12May 12, 2025Updated last year
- REcombination BARcode detector.☆17Apr 2, 2024Updated 2 years ago
- ☆10Jun 9, 2025Updated last year
- Iterate k-min-mers from a DNA sequence in Rust☆13Apr 8, 2024Updated 2 years ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆71Apr 10, 2025Updated last year
- ⚡️ 🧬 Fulgor is a fast and space-efficient colored de Bruijn graph index.☆59Sep 18, 2026Updated 3 weeks ago
- 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.
- CLI tool for querying the Genome Taxonomy Database (GTDB). Batch search, genome cards, taxon lineages, and cross-release taxonomic compar…☆33Sep 18, 2026Updated 3 weeks ago
- A comprehensive prokaryotic genome annotation pipeline☆92Updated this week
- Lemur is a tool for rapid and accurate taxonomic profiling on long-read metagenomic datasets☆25Apr 30, 2026Updated 5 months ago
- Reproducible research - Preparing code to be usable by you and others in the future☆36Oct 6, 2026Updated last week
- fast, multithreaded sourmash operations: search, compare, and gather.☆25Oct 5, 2026Updated last week
- Variant calling pipeline designed for Q20+ ONT long-reads☆15Updated this week
- ☆20Sep 16, 2026Updated 3 weeks ago
- Visualize genomic data using webgl and webworkers, in an effort to provide a fluid, high-performance user experience.☆11May 24, 2024Updated 2 years ago
- Modular job submitter for arbitrary pipelines or commands.☆26Oct 2, 2026Updated last week
- 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.
- Repository for codes, analyses and visualizations for the CAMI II challenges☆15Sep 4, 2023Updated 3 years ago
- iFISH Probe Design: a Python3 package to build iFISH probes.☆12Mar 11, 2022Updated 4 years ago
- strain-level analysis tools☆40Oct 21, 2024Updated last year
- Paint genomes with taxa-specific k-mer probabilities☆16Apr 4, 2022Updated 4 years ago
- Python library for volumetric data☆18Updated this week
- ☆12Jan 27, 2022Updated 4 years ago
- Python bindings for Bifrost's compacted colored de Bruijn Graph with a NetworkX-compatible API☆27Oct 20, 2023Updated 2 years ago