Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surroundin…
☆154Oct 2, 2025Updated 7 months ago
Alternatives and similar repositories for parsnp
Users that are interested in parsnp are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- An updated pipeline for pangenome investigation☆356Apr 22, 2026Updated last week
- ☆14Apr 15, 2026Updated 2 weeks ago
- Rapid & standardized annotation of bacterial genomes, MAGs & plasmids☆633Feb 18, 2026Updated 2 months ago
- A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome☆108Dec 5, 2025Updated 4 months ago
- MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies☆174Apr 16, 2025Updated last year
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.☆126Oct 30, 2023Updated 2 years ago
- Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins☆216Aug 27, 2025Updated 8 months ago
- Pairwise SNP distance matrix from a FASTA sequence alignment☆154Dec 31, 2025Updated 4 months ago
- Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.☆249Oct 12, 2025Updated 6 months ago
- Circular bacterial genome plots based on BLAST or NUCMER/PROMER alignments☆109Dec 11, 2023Updated 2 years ago
- Rapid large-scale prokaryote pan genome analysis☆377Nov 3, 2025Updated 5 months ago
- Prediction of prophages from bacterial genomes☆83Mar 17, 2026Updated last month
- Assemble bacterial isolate genomes from Nanopore reads☆131Jan 22, 2025Updated last year
- Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.☆106Jan 22, 2026Updated 3 months 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.
- Reorients assembled microbial sequences☆137Aug 21, 2025Updated 8 months ago
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆107Mar 2, 2026Updated 2 months ago
- BItsliced Genomic Signature Index - Efficient indexing and search in very large collections of WGS data☆10Jun 13, 2023Updated 2 years ago
- A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data☆71Feb 23, 2026Updated 2 months ago
- Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.☆198Apr 24, 2026Updated last week
- Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.☆121Jan 22, 2025Updated last year
- Fast genome and metagenome distance estimation using MinHash☆440Sep 19, 2025Updated 7 months ago
- ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.☆302Feb 3, 2026Updated 2 months ago
- Pan-genome wide association studies☆215May 29, 2024Updated last year
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Mass screening of contigs for antimicrobial and virulence genes☆491Apr 3, 2026Updated 3 weeks ago
- GrapeTree is a fully interactive, tree visualization program, which supports facile manipulations of both tree layout and metadata. Click…☆87Dec 15, 2024Updated last year
- Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.☆150Jan 9, 2026Updated 3 months ago
- A toolbox for pangenome analysis and threshold evaluation.☆100Jul 8, 2022Updated 3 years ago
- A pipeline for running AMRfinderPlus and collating results into functional classes☆94Mar 30, 2026Updated last month
- Fast Whole-Genome Similarity (ANI) Estimation☆454Dec 16, 2025Updated 4 months ago
- Antimicrobial Resistance Identification By Assembly☆187Oct 12, 2023Updated 2 years ago
- Bifrost graph gene caller.☆98Apr 12, 2026Updated 2 weeks ago
- A hybrid assembly and MAG recovery pipeline (and more!)☆106Updated this week
- 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.
- Finding regions of similarity between plasmids☆17Nov 2, 2022Updated 3 years ago
- Fast and precise comparison of genomes and metagenomes (in the order of terabytes) on a typical personal laptop☆74Apr 1, 2026Updated last month
- Create a tree using Mash distances☆188Oct 24, 2023Updated 2 years ago
- Build a partitioned pangenome graph from microbial genomes☆298Apr 20, 2026Updated last week
- A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences☆64Updated this week
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆121May 21, 2024Updated last year
- Recombination-free trees☆65Updated this week