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…
☆157Oct 2, 2025Updated 9 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☆365Jul 2, 2026Updated 2 weeks ago
- ☆14Jun 14, 2026Updated last month
- Rapid & standardized annotation of bacterial genomes, MAGs & plasmids☆663Jul 10, 2026Updated last week
- A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome☆115Dec 5, 2025Updated 7 months ago
- MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies☆179Apr 16, 2025Updated last year
- Simple, predictable pricing with DigitalOcean hosting • AdAlways know what you'll pay with monthly caps and flat pricing. Enterprise-grade infrastructure trusted by 600k+ customers.
- Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.☆259May 13, 2026Updated 2 months ago
- A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.☆128Oct 30, 2023Updated 2 years ago
- Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins☆221Aug 27, 2025Updated 10 months ago
- Pairwise SNP distance matrix from a FASTA sequence alignment☆156Dec 31, 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☆378Nov 3, 2025Updated 8 months ago
- Prediction of prophages from bacterial genomes☆87May 1, 2026Updated 2 months ago
- Assemble bacterial isolate genomes from Nanopore reads☆136Jan 22, 2025Updated last year
- Reorients assembled microbial sequences☆143Jun 30, 2026Updated 3 weeks ago
- 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.
- Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.☆107Jan 22, 2026Updated 6 months ago
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆109Jun 2, 2026Updated last month
- BItsliced Genomic Signature Index - Efficient indexing and search in very large collections of WGS data☆10Jun 13, 2023Updated 3 years ago
- A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences☆67Apr 30, 2026Updated 2 months ago
- Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.☆124May 29, 2026Updated last month
- Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.☆203Jun 10, 2026Updated last month
- A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data☆71Feb 23, 2026Updated 4 months ago
- Pan-genome wide association studies☆219May 29, 2024Updated 2 years ago
- Fast genome and metagenome distance estimation using MinHash☆447Sep 19, 2025Updated 10 months ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Mass screening of contigs for antimicrobial and virulence genes☆502Updated this week
- A toolbox for pangenome analysis and threshold evaluation.☆101Jul 8, 2022Updated 4 years ago
- GrapeTree is a fully interactive, tree visualization program, which supports facile manipulations of both tree layout and metadata. Click…☆90Updated this week
- Fast Whole-Genome Similarity (ANI) Estimation☆470Dec 16, 2025Updated 7 months ago
- Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.☆151Jul 4, 2026Updated 2 weeks ago
- Build a partitioned pangenome graph from microbial genomes☆307Jul 10, 2026Updated last week
- A pipeline for running AMRfinderPlus and collating results into functional classes☆100Jun 8, 2026Updated last month
- Antimicrobial Resistance Identification By Assembly☆186Oct 12, 2023Updated 2 years ago
- Making whole bacterial genome sequencing data analysis easy☆114Apr 22, 2025Updated last year
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- A hybrid assembly and MAG recovery pipeline (and more!)☆109Jul 10, 2026Updated last week
- Finding regions of similarity between plasmids☆17Jul 15, 2026Updated last week
- Fast and precise comparison of genomes and metagenomes (in the order of terabytes) on a typical personal laptop☆75Apr 1, 2026Updated 3 months ago
- Create a tree using Mash distances☆188Oct 24, 2023Updated 2 years ago
- AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and p…☆378Jul 12, 2026Updated last week
- A tool for generating consensus long-read assemblies for bacterial genomes☆345Sep 11, 2025Updated 10 months ago
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆124Jun 2, 2026Updated last month