Compute strain abundance in a defined microbial community
☆10Jul 27, 2023Updated 2 years ago
Alternatives and similar repositories for ninjaMap
Users that are interested in ninjaMap are comparing it to the libraries listed below
Sorting:
- accessory functions for processing microbial community data☆12Dec 24, 2022Updated 3 years ago
- Fast tool to build the core genome of prokaryotic genomes. Can handle large datasets. Dependencis: Usearch & Numpy☆10Nov 26, 2025Updated 3 months ago
- Development repo for pyani-plus (the next iteration of pyani)☆24Feb 18, 2026Updated last week
- supplementary tables and files☆10Oct 13, 2023Updated 2 years ago
- Just another minhash implementation.☆12Updated this week
- ☆15Jan 28, 2026Updated 3 weeks ago
- Needleman-Wunsch Alignment in Go☆12Nov 9, 2020Updated 5 years ago
- Automated synthetic microbial Community Design☆13Mar 26, 2021Updated 4 years ago
- 2025 RAD microbes boot camp☆15Apr 30, 2025Updated 9 months ago
- Embedding-based indexing for compact storage and rapid querying of bacterial pan-genomes☆21Dec 9, 2025Updated 2 months ago
- Rust crate to deal with phylogenetic trees☆14Dec 3, 2025Updated 2 months ago
- Ultra-rapid detection of viral variants directly from sequencing data☆35Feb 17, 2026Updated last week
- ☆15Dec 8, 2022Updated 3 years ago
- MUSiCC: A marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome☆16Nov 7, 2019Updated 6 years ago
- Tools for phylogenetic data analysis including visualization and cluster-computing support.☆14Dec 18, 2021Updated 4 years ago
- Host depletion optimised for clinical metagenomic sequencing applications☆16Nov 18, 2024Updated last year
- Shared k-mer content between two genomes☆19Jun 21, 2023Updated 2 years ago
- Next Index to Query Kmer Intersection☆17Feb 1, 2023Updated 3 years ago
- Fast and Memory Efficient Genome Sketching via HyperLogLog, HyperMinHash and UltraLogLog☆19Jan 22, 2026Updated last month
- GTDB => NCBI☆15Nov 14, 2024Updated last year
- ☆17Nov 19, 2024Updated last year
- Minimum plain text representation of kmer sets☆16Jan 30, 2025Updated last year
- COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)☆20Nov 24, 2024Updated last year
- complex Chaos Game Representation for DNA sequences☆21Apr 3, 2025Updated 10 months ago
- Kraken2 Server☆23Nov 24, 2025Updated 3 months ago
- ☆19Dec 15, 2020Updated 5 years ago
- Parallel Construction of Suffix Arrays in Rust☆26May 2, 2025Updated 9 months ago
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆20Apr 20, 2023Updated 2 years ago
- A Rust library for parsing, writing and manipulating Genbank sequence files☆22Apr 20, 2025Updated 10 months ago
- BACTpipe: An assembly and annotation pipeline for bacterial genomics☆20Dec 3, 2024Updated last year
- [AAAI'22] RepBin: Constraint-Based Graph Representation Learning for Metagenomic Binning☆25Jan 26, 2024Updated 2 years ago
- A FASTA/FASTQ format parser library☆20Mar 1, 2024Updated last year
- Fast viral consensus genome reconstruction☆25Feb 5, 2026Updated 3 weeks ago
- QIIME 2 plugin wrapping DADA2☆22Jan 27, 2026Updated last month
- Generate kmers/minimizers/hashes/MinHash signatures, including with multiple kmer sizes.☆24Jan 9, 2021Updated 5 years ago
- k-SLAM ultra fast alignment and taxonomic classification of metagenomic datasets☆23Nov 18, 2018Updated 7 years ago
- MDMcleaner the assessment, classification and refinement tool for microbial dark matter SAGs and MAGs☆25Mar 19, 2023Updated 2 years ago
- Reference Phylogeny for Bacterial and Archaeal Genomes☆25Aug 9, 2025Updated 6 months ago
- fast, multithreaded sourmash operations: search, compare, and gather.☆25Updated this week