Embedding-based indexing for compact storage and rapid querying of bacterial pan-genomes
☆21Dec 9, 2025Updated 2 months ago
Alternatives and similar repositories for panspace
Users that are interested in panspace are comparing it to the libraries listed below
Sorting:
- ☆15Jan 28, 2026Updated last month
- complex Chaos Game Representation for DNA sequences☆21Apr 3, 2025Updated 10 months ago
- 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 last year
- Fast tool to build the core genome of prokaryotic genomes. Can handle large datasets. Dependencis: Usearch & Numpy☆10Nov 26, 2025Updated 3 months ago
- R integration for edlib, a C/C++ library for pairwise sequence alignment using edit distance (Levenshtein distance).☆11Jul 20, 2025Updated 7 months ago
- Code to create a PRG from a Multiple Sequence Alignment file☆25Sep 10, 2025Updated 5 months ago
- Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)☆41Apr 17, 2024Updated last year
- Strain-level haplotyping for metagenomes with short or long-reads.☆64Apr 10, 2025Updated 10 months ago
- Mapping NCBI Genbank accession to GTDB accession☆14Feb 13, 2021Updated 5 years ago
- Approximate nearest neighbour search for microbial genomes based on hash metric☆59Dec 14, 2025Updated 2 months ago
- Host depletion optimised for clinical metagenomic sequencing applications☆16Nov 18, 2024Updated last year
- Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes☆71Dec 1, 2025Updated 3 months ago
- Next Index to Query Kmer Intersection☆17Feb 1, 2023Updated 3 years ago
- PanPA is a tool for building panproteome graphs and aligning sequences back to the graphs.☆18Feb 2, 2025Updated last year
- Discover and annotate the virome☆59Feb 11, 2026Updated 2 weeks ago
- Phage-Host Interaction Search Tool☆29Jul 8, 2024Updated last year
- Downstream processing of VAMB binning for Viral Elucidation☆54Jul 3, 2024Updated last year
- Space-efficient pseudoalignment with a colored de Bruijn graph☆52Mar 13, 2025Updated 11 months ago
- COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)☆20Nov 24, 2024Updated last year
- Minimum plain text representation of kmer sets☆16Jan 30, 2025Updated last year
- MetagenOmic read Re-Assigner and abundance quantifier☆20Jan 31, 2025Updated last year
- ☆22Dec 9, 2023Updated 2 years ago
- Unified Human Gut Virome Catalog☆41Nov 10, 2025Updated 3 months ago
- FMSI is a highly memory efficient exact k-mer set index based on masked superstrings and the masked Burrows-Wheeler transform☆23Nov 20, 2025Updated 3 months ago
- Logan Unitigs and Contigs☆184Sep 14, 2025Updated 5 months ago
- Pipeline for major biological analyses.☆36Mar 30, 2022Updated 3 years ago
- Compute strain abundance in a defined microbial community☆10Jul 27, 2023Updated 2 years ago
- Grabbing genome accessions & download info based on taxonomy, using the NCBI REST API, w00t☆12Feb 23, 2025Updated last year
- Multiple Bacteria Genome Compressor (MBGC)☆11Feb 20, 2026Updated last week
- Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]☆47Apr 1, 2025Updated 11 months ago
- De novo VIral Genome Annotator☆24Jan 11, 2026Updated last month
- Linear Decomposition Model☆25Jun 16, 2023Updated 2 years ago
- Index kmtricks bf matrices☆46Feb 13, 2026Updated 2 weeks ago
- Fast viral consensus genome reconstruction☆25Feb 5, 2026Updated 3 weeks ago
- ✨🧬 Refined binning of metagenomic contigs using assembly graphs☆97Mar 6, 2025Updated 11 months ago
- MetaMDBG: a lightweight assembler for long and accurate metagenomics reads.☆203Feb 16, 2026Updated last week
- ☆46Nov 21, 2025Updated 3 months ago
- ☆11Mar 10, 2024Updated last year
- Predict prokaryotic hosts for phage (meta) genomic sequences☆11Apr 4, 2022Updated 3 years ago