A pipeline for high-quality bacterial genome construction using ONT sequencing
☆38Sep 22, 2022Updated 3 years ago
Alternatives and similar repositories for micropipe
Users that are interested in micropipe are comparing it to the libraries listed below
Sorting:
- A scalable bacterial genome assembly, annotation and analysis pipeline☆74Dec 5, 2023Updated 2 years ago
- hAMRoaster is an analysis pipeline that can compare the output of tools for detecting AMR genes and provide metrics of their performance☆22Mar 8, 2024Updated last year
- Generate basic stats for an assembly.☆13Feb 12, 2023Updated 3 years ago
- Finding regions of similarity between plasmids☆17Nov 2, 2022Updated 3 years ago
- A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates☆13Aug 26, 2024Updated last year
- High-quality Nanopore-only genome polisher☆69Aug 16, 2024Updated last year
- Targeted Detection and Reconstruction of Plasmids☆22May 7, 2024Updated last year
- Predict plasmids from uncorrected long read data☆41Oct 31, 2025Updated 4 months ago
- rapid serotyping of Vibrio parahaemolyticus from whole genome sequencing data using serogroup-specific genes☆10Sep 2, 2021Updated 4 years ago
- Rapid identification of Staphylococcus aureus agr locus type and agr operon variants.☆10Jan 6, 2023Updated 3 years ago
- Output FASTQ summary statistics in JSON format☆29Oct 30, 2022Updated 3 years ago
- Assemble bacterial isolate genomes from Nanopore reads☆128Jan 22, 2025Updated last year
- Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies☆12Jun 30, 2023Updated 2 years ago
- Visualisation application for Klebsiella genotypes generated by Kleborate.☆10Sep 27, 2025Updated 5 months ago
- The Whole Genome Sequencing Coverage Plot (wgscovplot) is a tool to generate HTML Interactive Coverage Plot given coverage depth informat…☆19May 3, 2024Updated last year
- CFSAN Shigella Typing Pipeline☆15Jul 6, 2023Updated 2 years ago
- UPHL's Reference Free Pipeline☆27Feb 21, 2026Updated last week
- Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads☆64Jan 22, 2026Updated last month
- Dryad is a Nextflow pipeline for examining prokaryote relatedness. Dryad can perform a reference free analysis and/or SNP analysis.☆18Nov 20, 2025Updated 3 months ago
- A nextflow version of the Wochenende reference metagenome binning and visualization pipeline☆15Dec 14, 2024Updated last year
- k-mer based Pipeline to identify the Serotype from Illumina NGS reads☆26Jul 13, 2023Updated 2 years ago
- whole genome MLST analysis☆52Jun 13, 2025Updated 8 months ago
- LYVE-SET, a method of using hqSNPs to create a phylogeny, especially for outbreak investigations☆27Aug 26, 2024Updated last year
- MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies☆168Apr 16, 2025Updated 10 months ago
- Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data☆13Jun 12, 2024Updated last year
- A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences☆63Nov 20, 2025Updated 3 months ago
- ☆27Aug 2, 2023Updated 2 years ago
- Phylogeny Enhanded Prediction of PAN-genome☆43Jul 17, 2020Updated 5 years ago
- software to identify primers that can distinguish genomes☆20Jan 23, 2026Updated last month
- SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity☆13Aug 14, 2023Updated 2 years ago
- Development version of Easyfig☆105Dec 21, 2023Updated 2 years ago
- Reorients assembled microbial sequences☆133Aug 21, 2025Updated 6 months ago
- tool to determine optimal refrerence genome given a set of fasta files☆15May 18, 2023Updated 2 years ago
- A tool for removing redundant genomes from a set of assemblies☆78Sep 10, 2025Updated 5 months ago
- ☆13May 27, 2025Updated 9 months ago
- zDB: comparative bacterial genomics made easy☆38Feb 2, 2026Updated 3 weeks ago
- Bacterial analysis toolbox for full ESKAPE pathogen characterization and profiling the resistome, mobilome, virulome & phylogenomics usin…☆26Jan 30, 2025Updated last year
- Intra-species bacterial contamination detection☆25Feb 5, 2026Updated 3 weeks ago
- A taxonomic classifier of plasmids☆28Jul 7, 2021Updated 4 years ago