Embedding-based indexing for compact storage and rapid querying of bacterial pan-genomes
☆22Jun 9, 2026Updated this week
Alternatives and similar repositories for panspace
Users that are interested in panspace are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)☆41Apr 17, 2024Updated 2 years ago
- ☆15Jan 28, 2026Updated 4 months ago
- R integration for edlib, a C/C++ library for pairwise sequence alignment using edit distance (Levenshtein distance).☆11Jul 20, 2025Updated 10 months ago
- complex Chaos Game Representation for DNA sequences☆21Apr 3, 2025Updated last year
- Mapping NCBI Genbank accession to GTDB accession☆14Feb 13, 2021Updated 5 years ago
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- Strain-level haplotyping for metagenomes with short or long-reads.☆66Apr 10, 2025Updated last year
- Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]☆47Apr 1, 2025Updated last year
- Map query sequences to the assemblies of all pre-June 2023 bacteria (https://ftp.ebi.ac.uk/pub/databases/AllTheBacteria/Releases/0.2/) on…☆12May 22, 2024Updated 2 years ago
- Fast tool to build the core genome of prokaryotic genomes. Can handle large datasets. Dependencis: Usearch & Numpy☆10Nov 26, 2025Updated 6 months ago
- Code to create a PRG from a Multiple Sequence Alignment file☆25Sep 10, 2025Updated 8 months ago
- Approximate nearest neighbour search for microbial genomes based on hash metric☆66Mar 7, 2026Updated 3 months ago
- Downstream processing of VAMB binning for Viral Elucidation☆55Jul 3, 2024Updated last year
- Phage-Host Interaction Search Tool☆31Jul 8, 2024Updated last year
- Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes☆74Dec 1, 2025Updated 6 months ago
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- Host depletion optimised for clinical metagenomic sequencing applications☆18May 18, 2026Updated 3 weeks ago
- Next Index to Query Kmer Intersection☆17Feb 1, 2023Updated 3 years ago
- MetagenOmic read Re-Assigner and abundance quantifier☆20Jan 31, 2025Updated last year
- Plasmid analysis using rearrangement distances☆55May 28, 2026Updated last week
- ☆22Dec 9, 2023Updated 2 years ago
- ProphAsm – a rapid computation of simplitigs directly from k-mer sets☆25Feb 17, 2023Updated 3 years ago
- Index kmtricks bf matrices☆49Apr 29, 2026Updated last month
- ☆47May 12, 2026Updated 3 weeks ago
- Rapid estimation of phylogenetic trees using sketching☆13Feb 18, 2025Updated last year
- 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.
- Discover and annotate the virome☆63Feb 11, 2026Updated 3 months ago
- Strain-level abundances estimation in metagenomic samples using variation graphs☆24Jan 29, 2023Updated 3 years ago
- PanPA is a tool for building panproteome graphs and aligning sequences back to the graphs.☆19Apr 9, 2026Updated 2 months ago
- Space-efficient pseudoalignment with a colored de Bruijn graph☆55Mar 13, 2025Updated last year
- Grabbing genome accessions & download info based on taxonomy, using the NCBI REST API, w00t☆12Feb 23, 2025Updated last year
- Paired reads mapping on de Bruijn graph☆13Jan 15, 2019Updated 7 years ago
- Minimum plain text representation of kmer sets☆18Jan 30, 2025Updated last year
- COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)☆20Nov 24, 2024Updated last year
- MetaMDBG: a lightweight assembler for long and accurate metagenomics reads.☆221May 9, 2026Updated last month
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- genome simulation across a population with zeta-distributed allele frequency, snps, insertions, deletions, and multi-nucleotide polymorph…☆16Mar 3, 2022Updated 4 years ago
- A Hierarchical Approach to Pangenomics Inference☆13Apr 15, 2024Updated 2 years ago
- FMSI is a highly memory efficient exact k-mer set index based on masked superstrings and the masked Burrows-Wheeler transform☆24Nov 20, 2025Updated 6 months ago
- Discovery of conserved gene clusters in multiple genomes☆132Jan 16, 2026Updated 4 months ago
- ☆12May 6, 2022Updated 4 years ago
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆27Jul 22, 2024Updated last year
- Pipeline for major biological analyses.☆35Mar 30, 2022Updated 4 years ago