tongzhouxu / mashpitView external linksLinks
Sketch-based surveillance platform
☆13Dec 17, 2024Updated last year
Alternatives and similar repositories for mashpit
Users that are interested in mashpit are comparing it to the libraries listed below
Sorting:
- Just another minhash implementation.☆12Updated this week
- ☆10Jun 16, 2022Updated 3 years ago
- app to collapse Pango lineages for reporting☆12Dec 9, 2025Updated 2 months ago
- ☆27May 22, 2025Updated 8 months ago
- Experiments with using BIGSI data structure for metagenomic and QC applications☆19Aug 12, 2024Updated last year
- Ultra-rapid detection of viral variants directly from sequencing data☆34Feb 6, 2026Updated last week
- Next Index to Query Kmer Intersection☆17Feb 1, 2023Updated 3 years ago
- SeqSero2☆39Oct 1, 2025Updated 4 months ago
- Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.☆13Dec 24, 2025Updated last month
- Benchmark datasets for WGS analysis☆39Aug 4, 2019Updated 6 years ago
- Fast, scalable, accurate and accessible Bayesian phylogenetics☆41Updated this week
- fast, multithreaded sourmash operations: search, compare, and gather.☆25Feb 9, 2026Updated last week
- NCBI Pathogen Detection Portal toolkit☆11Sep 6, 2023Updated 2 years ago
- Validation of sycnmers compared to minimizers☆11May 10, 2025Updated 9 months ago
- interactive barplot for amplicon sequencing☆13Dec 5, 2024Updated last year
- ☆10Apr 16, 2025Updated 10 months ago
- SeqWho - A reliable and rapid FASTQ(A) file classifier☆10Jan 21, 2022Updated 4 years ago
- Private, browser-based placement of genome sequences on phylogenetic trees using UShER.☆11Nov 22, 2024Updated last year
- Day 2 of ACAD's 2018 Advanced Bioinformatics Workshop☆12Nov 27, 2018Updated 7 years ago
- Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies☆12Jun 30, 2023Updated 2 years ago
- ☆10Dec 16, 2024Updated last year
- Static website for the PH4AGE alliance☆13Oct 27, 2023Updated 2 years ago
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆103Feb 9, 2026Updated last week
- Rapid determination of appropriate reference genomes.☆99Jan 22, 2025Updated last year
- use variant nesting information to flter overlapping sites from vg deconstruct output☆31Jun 12, 2025Updated 8 months ago
- Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can b…☆149Oct 2, 2025Updated 4 months ago
- the we-flyin WFA-guided ultralong tiling sequence aligner☆10May 13, 2021Updated 4 years ago
- DartMinHash: Fast Sketching for Weighted Sets☆12Dec 8, 2025Updated 2 months ago
- A Nextflow pipeline for genome and pan-genome annotation☆15Feb 3, 2026Updated 2 weeks ago
- Reference implementations of minimizer schemes to go with the mod-minimizers paper.☆28Apr 24, 2025Updated 9 months ago
- Space-efficient pseudoalignment with a colored de Bruijn graph☆52Mar 13, 2025Updated 11 months ago
- Refinements of the WFA alignment algorithm with better complexity☆26Mar 31, 2022Updated 3 years ago
- A curated database of completed assemblies with taxonomy IDs☆48Updated this week
- Order and orientation of complete bacterial genomes☆29Jul 11, 2025Updated 7 months ago
- Iterate k-min-mers from a DNA sequence in Rust☆13Apr 8, 2024Updated last year
- Code for the paper Aligning Distant Sequences to Graphs using Long Seed Sketches.☆13Nov 1, 2022Updated 3 years ago
- Ampseer examines reads in fastq format and identifies which multiplex PCR primer set was used to generate the SARS-CoV-2 sequencing libra…☆15Feb 27, 2024Updated last year
- Archived - please see updated sccmec tool at link below☆13Aug 30, 2024Updated last year
- QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run☆12Dec 2, 2024Updated last year