This RAPT repository has been retired as of December 2024. NCBI's Read assembly and Annotation Pipeline Tool (RAPT) was a pilot service.
☆58Apr 1, 2025Updated last year
Alternatives and similar repositories for rapt
Users that are interested in rapt are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- SKESA assembler☆126Oct 11, 2024Updated last year
- NCBI Prokaryotic Genome Annotation Pipeline☆376Updated this week
- The NCBI SARS-CoV-2 Variant Calling (SC2VC) Pipeline allows calling high-confidence variants from SARS-CoV-2 NGS data in a standardized f…☆14Apr 21, 2023Updated 3 years ago
- Utility to analyse a group of closely related MAgs/Genomes/bins/SUBs of more or less dubious origin☆15Sep 24, 2024Updated last year
- 🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables☆29Feb 12, 2026Updated 2 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.
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Jun 26, 2018Updated 7 years ago
- StxTyper uses a standardized algorithm to accurately type both known and unknown Shiga toxin operons from assembled genomic sequence.☆16Apr 22, 2026Updated last week
- 🦠🧬🧑💻📇 Microbial genomes-to-report pipeline☆74Mar 14, 2026Updated last month
- MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions using protein family predictions, achiev…☆24Jun 9, 2021Updated 4 years ago
- Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.☆106Jan 22, 2026Updated 3 months ago
- genome_updater is a bash script that downloads and updates (non-redundant) snapshots of the NCBI Genomes repository (RefSeq/GenBank) with…☆168Apr 22, 2026Updated last week
- AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and p…☆359Mar 29, 2026Updated last month
- A flexible pipeline for complete analysis of bacterial genomes☆504Updated this week
- "Reads to report" for public health and clinical microbiology☆142Dec 9, 2025Updated 4 months ago
- End-to-end encrypted cloud storage - Proton Drive • AdSpecial offer: 40% Off Yearly / 80% Off First Month. Protect your most important files, photos, and documents from prying eyes.
- Reference Phylogeny for Bacterial and Archaeal Genomes☆25Aug 9, 2025Updated 8 months ago
- Collection of R scripts for SARS-CoV-2 (variant) analyses☆12Mar 2, 2023Updated 3 years ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆60Nov 3, 2023Updated 2 years ago
- Assessing the quality of prokaryotic genomes, filtering and dereplication☆11Aug 26, 2022Updated 3 years ago
- PANgenome with Annotations, COre identification, Tree and corresponding Alignments☆81Sep 20, 2023Updated 2 years ago
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆27Sep 7, 2019Updated 6 years ago
- In silico serotyping, finetyping and Bexsero antigen sequence typing of Neisseria meningitidis☆15Feb 19, 2026Updated 2 months ago
- Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotation☆114Mar 5, 2026Updated last month
- Rapid & standardized annotation of bacterial genomes, MAGs & plasmids☆633Feb 18, 2026Updated 2 months ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆35Dec 4, 2025Updated 4 months ago
- Intra-species bacterial contamination detection☆25Apr 13, 2026Updated 2 weeks ago
- Predict plasmids from uncorrected long read data☆41Feb 27, 2026Updated 2 months ago
- An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and…☆54Jul 24, 2025Updated 9 months ago
- BRIG is a cross-platform (Windows/Mac/Linux) application that displays circular comparison images of multiple genomes using BLAST.☆47Apr 4, 2026Updated 3 weeks ago
- Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins☆216Aug 27, 2025Updated 8 months ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆43Dec 11, 2020Updated 5 years ago
- Antibiotic resistance prediction in minutes☆115Mar 27, 2026Updated last month
- Gene cluster comparison figure generator☆640Dec 22, 2025Updated 4 months ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Split Kmer Analysis☆66May 26, 2022Updated 3 years ago
- Protologgger is a tool for the description of novel taxa by providing taxonomic, functional and ecological insights☆17Nov 24, 2025Updated 5 months ago
- Database and pipeline for protein structure-guided annotations of ecologically relevant functions at the metagenome scale.☆24Nov 2, 2025Updated 6 months ago
- Rapid identification of Staphylococcus aureus agr locus type and agr operon variants.☆11Jan 6, 2023Updated 3 years ago
- Python package for detection of chimerism and contamination in prokaryotic genomes.☆89Mar 12, 2026Updated last month
- A tool for generating consensus long-read assemblies for bacterial genomes☆342Sep 11, 2025Updated 7 months ago
- Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure☆176Apr 22, 2026Updated last week