A method for reconstruction of subspecies composition and functional profiles from metagenomic data
☆13May 27, 2024Updated 2 years ago
Alternatives and similar repositories for StrainPanDA
Users that are interested in StrainPanDA are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆10Jun 9, 2020Updated 6 years ago
- Next Index to Query Kmer Intersection☆17Feb 1, 2023Updated 3 years ago
- Find Co-Abundant Groups of Genes☆12Aug 3, 2020Updated 6 years ago
- Strain-level abundances estimation in metagenomic samples using variation graphs☆24Jan 29, 2023Updated 3 years ago
- A healthy human gut genome collection☆26Aug 21, 2025Updated last year
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Mapping NCBI Genbank accession to GTDB accession☆14Feb 13, 2021Updated 5 years ago
- Alignment algorithm for short Illumina reads to a de Bruijn graph☆17Jun 4, 2019Updated 7 years ago
- R markdown documents copied from other folders on Dec 15th 2021☆14Nov 4, 2025Updated 11 months ago
- Code for the paper Aligning Distant Sequences to Graphs using Long Seed Sketches.☆13Nov 1, 2022Updated 4 years ago
- Implementation of the u-index☆12Jul 19, 2025Updated last year
- Space-efficient pseudoalignment with a colored de Bruijn graph☆59Mar 13, 2025Updated last year
- Metalign: efficient alignment-based metagenomic profiling via containment min hash☆31Sep 12, 2023Updated 3 years ago
- NCBI Taxonomy History Browser☆10May 7, 2026Updated 5 months ago
- Iterate k-min-mers from a DNA sequence in Rust☆13Apr 8, 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.
- Raspir, the rare species identifier☆11Oct 19, 2023Updated 3 years ago
- Support scripts for the visualisation of pangenome analyses in Graphia☆22Oct 7, 2024Updated 2 years ago
- Needleman-Wunsch Alignment in Go☆12Nov 9, 2020Updated 5 years ago
- Sketch-based surveillance platform☆13Updated this week
- Whole genome focused array SNP typer☆14Feb 2, 2026Updated 9 months ago
- Importing vg json graphs to Python data structures.☆12Nov 11, 2020Updated 5 years ago
- Viral genome coverage evaluation for metagenomic diagnostics☆27Jul 9, 2026Updated 3 months ago
- CLI tool for querying the Genome Taxonomy Database (GTDB). Batch search, genome cards, taxon lineages, and cross-release taxonomic compar…☆33Sep 18, 2026Updated last month
- ☆14Jul 30, 2026Updated 3 months ago
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- FMSI is a highly memory efficient exact k-mer set index based on masked superstrings and the masked Burrows-Wheeler transform☆25Nov 20, 2025Updated 11 months ago
- ☆14Oct 14, 2020Updated 6 years ago
- ViromeScan allows the user to explore and taxonomically characterize the virome from metagenomic reads, efficiently denoising samples fro…☆13Feb 13, 2023Updated 3 years ago
- Compressed, associative, and exact hash table for k-mers☆11Oct 15, 2026Updated 2 weeks ago
- metagenome population recombination rate estimation pipeline☆12Nov 23, 2025Updated 11 months ago
- Tool intended to pull out sequences and annotations between insertion sites specified by the user.☆15Apr 10, 2026Updated 6 months ago
- Scalable creating/updating of metagenome profiling databases☆62Jun 25, 2025Updated last year
- Interactive tree visualizations in Python (powered by Vega).☆11Sep 26, 2019Updated 7 years ago
- ☆11Mar 11, 2025Updated last year
- 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.
- Accurate metagenomic profiling && Fast large-scale sequence/genome searching☆221Apr 24, 2026Updated 6 months ago
- Metagenomic profiling and phylogenetic distances via common kmers☆41Jul 12, 2021Updated 5 years ago
- De novo metagenome assembler☆15Mar 29, 2023Updated 3 years ago
- Recording personal workflows used in work, study notes, and summaries of various tools and methods.☆11Oct 9, 2025Updated last year
- Hierarchical Unique Bait Design for simultaneous and specific capture of known and novel targets☆18Sep 19, 2023Updated 3 years ago
- Shared k-mer content between two genomes☆18Jun 21, 2023Updated 3 years ago
- Software used to develop the TCMA database associated with 10.1016/j.chom.2020.12.001.☆15Nov 26, 2023Updated 2 years ago