A scalable bacterial genome assembly, annotation and analysis pipeline
☆79Dec 5, 2023Updated 2 years ago
Alternatives and similar repositories for asap
Users that are interested in asap are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- A pipeline for high-quality bacterial genome construction using ONT sequencing☆40Sep 22, 2022Updated 3 years ago
- Making whole bacterial genome sequencing data analysis easy☆115Apr 22, 2025Updated last year
- A flexible pipeline for complete analysis of bacterial genomes☆522Aug 5, 2026Updated 3 weeks ago
- ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads☆264Jun 11, 2026Updated 2 months ago
- Rapid determination of appropriate reference genomes.☆103Jan 22, 2025Updated last year
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- BACTpipe: An assembly and annotation pipeline for bacterial genomics☆20Aug 13, 2026Updated 2 weeks ago
- "Reads to report" for public health and clinical microbiology☆144Dec 9, 2025Updated 8 months ago
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆109Jun 2, 2026Updated 3 months ago
- A tool for generating consensus long-read assemblies for bacterial genomes☆348Jul 24, 2026Updated last month
- Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.☆129Aug 6, 2026Updated 3 weeks ago
- Predict MLST directly from uncorrected long reads☆27Oct 31, 2025Updated 10 months ago
- Pipeline for analysing intergenic regions in bacteria☆39Oct 25, 2019Updated 6 years ago
- An updated pipeline for pangenome investigation☆374Jul 2, 2026Updated 2 months ago
- Short Read Sequence Typing for Bacterial Pathogens☆149Jun 20, 2021Updated 5 years ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Genomic neighbor typing of bacterial pathogens using MinHash☆42Jan 10, 2023Updated 3 years ago
- Assemble bacterial isolate genomes from Nanopore reads☆136Jan 22, 2025Updated last year
- A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates☆15Aug 26, 2024Updated 2 years ago
- Automated strain separation of low-complexity metagenomes☆52Nov 10, 2021Updated 4 years ago
- Antimicrobial Resistance Identification By Assembly☆186Oct 12, 2023Updated 2 years ago
- The MLST pipeline developed by the PathOGiST research group☆39Nov 29, 2023Updated 2 years ago
- A toolbox for pangenome analysis and threshold evaluation.☆101Jul 8, 2022Updated 4 years ago
- Ultrafast sequence typing and gene detection from NGS raw reads☆20Apr 15, 2021Updated 5 years ago
- Rapid & standardized annotation of bacterial genomes, MAGs & plasmids☆670Aug 7, 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.
- Bacterial analysis toolbox for full ESKAPE pathogen characterization and profiling the resistome, mobilome, virulome & phylogenomics usin…☆27Jan 30, 2025Updated last year
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆30Jul 18, 2025Updated last year
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆47Aug 20, 2025Updated last year
- High-quality Nanopore-only genome polisher☆71Aug 16, 2024Updated 2 years ago
- A (very) fast program for getting statistics about a fastq file, the way I need them, written in Rust☆34Jul 27, 2026Updated last month
- Intra-species bacterial contamination detection☆26Jul 10, 2026Updated last month
- A pipeline for running AMRfinderPlus and collating results into functional classes☆102Updated this week
- ☆11May 14, 2025Updated last year
- rapid serotyping of Vibrio parahaemolyticus from whole genome sequencing data using serogroup-specific genes☆10Sep 2, 2021Updated 5 years ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Reorients assembled microbial sequences☆145Jun 30, 2026Updated 2 months ago
- CFSAN Shigella Typing Pipeline☆15Jun 11, 2026Updated 2 months ago
- Accurate metagenomic profiling && Fast large-scale sequence/genome searching☆220Apr 24, 2026Updated 4 months ago
- Dryad is a Nextflow pipeline for examining prokaryote relatedness. Dryad can perform a reference free analysis and/or SNP analysis.☆21Aug 17, 2026Updated 2 weeks ago
- ☆20Dec 7, 2020Updated 5 years ago
- A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences☆67Jul 27, 2026Updated last month
- Scan contig files against PubMLST typing schemes☆298Jun 17, 2026Updated 2 months ago