a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
☆67Jun 16, 2025Updated last year
Alternatives and similar repositories for Core-SNP-filter
Users that are interested in Core-SNP-filter are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆38Updated this week
- NCBI Pathogen Detection Portal toolkit☆11Sep 6, 2023Updated 3 years ago
- Plasmid analysis using rearrangement distances☆56Jul 19, 2026Updated 2 months ago
- Recombination-free trees☆74Jul 24, 2026Updated 2 months ago
- Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates☆91Sep 9, 2026Updated last month
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆25Jun 17, 2022Updated 4 years ago
- Fast pairwise transmission inference from single genome and/or metagenomic data☆39Aug 21, 2026Updated last month
- Bifrost graph gene caller.☆102Aug 31, 2026Updated last month
- A new high-resolution long-read metagenome assembler for even noisy reads☆173Oct 1, 2026Updated last week
- Reorients assembled microbial sequences☆145Jun 30, 2026Updated 3 months ago
- A Python package to update the MLST database for the mlst tool.☆33Jul 22, 2026Updated 2 months ago
- Finding regions of similarity between plasmids☆17Jul 15, 2026Updated 2 months ago
- Graph-based assembly phasing☆102Nov 25, 2025Updated 10 months ago
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆112Jun 2, 2026Updated 4 months ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- emm Automatic Isolate Labeller☆16Mar 25, 2025Updated last year
- Compute a pairwise SNP distance matrix from one or two alignment(s)☆27Sep 12, 2024Updated 2 years ago
- Create a tree using Mash distances☆191Oct 24, 2023Updated 2 years ago
- Bacterial surveillance pipeline.☆30Sep 30, 2026Updated last week
- Inferring global and local strict molecular clocks using root-to-tip regression☆20Jun 30, 2026Updated 3 months ago
- Dryad is a Nextflow pipeline for examining prokaryote relatedness. Dryad can perform a reference free analysis and/or SNP analysis.☆21Updated this week
- a short-read polishing tool for long-read assemblies☆226Jul 28, 2026Updated 2 months ago
- Simple-to-use interactive comparison of two bacterial genomes☆28Jan 30, 2026Updated 8 months ago
- Extracts contigs harbouring a target gene / sequence from assemblies and aligns the contigs around the target sequence☆13May 15, 2018Updated 8 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Analysing the genomic context of mobile genes☆11Jul 21, 2025Updated last year
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Jun 9, 2026Updated 4 months ago
- Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.☆264May 13, 2026Updated 4 months ago
- Precise host read removal☆132Apr 13, 2026Updated 5 months ago
- Fast long-read mapper and whole-genome aligner (accelerated version of minimap2)☆63Jul 5, 2026Updated 3 months ago
- Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.☆156Jul 24, 2026Updated 2 months ago
- A tool for generating consensus long-read assemblies for bacterial genomes☆240Oct 2, 2026Updated last week
- MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies☆187Apr 16, 2025Updated last year
- Genome size estimation from long read overlaps☆98Sep 8, 2026Updated last month
- 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.
- LexicMap: efficient sequence alignment against millions of prokaryotic genomes☆226Updated this week
- A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data☆51Sep 25, 2026Updated 2 weeks ago
- Assemble bacterial isolate genomes from Nanopore reads☆136Jan 22, 2025Updated last year
- Rapid haploid variant calling and core genome alignment☆594Dec 12, 2025Updated 9 months ago
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆48Sep 9, 2026Updated last month
- Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/articles/13821/)☆61Mar 23, 2023Updated 3 years ago
- An updated pipeline for pangenome investigation☆375Jul 2, 2026Updated 3 months ago