A toolkit for prokaryotic comparative genomics
☆51Feb 23, 2026Updated 3 weeks ago
Alternatives and similar repositories for SCARAP
Users that are interested in SCARAP are comparing it to the libraries listed below
Sorting:
- Functions to manipulate and visualize microbial community data☆12Sep 15, 2023Updated 2 years ago
- Functions to manipulate and visualize microbial community data☆13Mar 11, 2026Updated last week
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆54Sep 7, 2025Updated 6 months ago
- Finding regions of similarity between plasmids☆17Nov 2, 2022Updated 3 years ago
- Map query sequences to the assemblies of all pre-June 2023 bacteria (https://ftp.ebi.ac.uk/pub/databases/AllTheBacteria/Releases/0.2/) on…☆12May 22, 2024Updated last year
- Plasmid and antimicrobial resistance pipeline☆16Dec 30, 2024Updated last year
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆26Apr 5, 2024Updated last year
- zDB: comparative bacterial genomics made easy☆40Feb 2, 2026Updated last month
- Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.☆106Jan 22, 2026Updated last month
- The Prokaryotic Genomics and Comparative Genomics Analysis Pipeline☆41Dec 8, 2022Updated 3 years ago
- Pipeline detecting distant and putative novel insertion sequences in prokaryotic genomes☆13Jun 10, 2021Updated 4 years ago
- A toolbox for comparative genomics.☆109May 26, 2021Updated 4 years ago
- 🦠🧬🧑💻📇 Microbial genomes-to-report pipeline☆74Mar 13, 2026Updated last week
- Hybrid Assembler for Plasmids☆10Jul 28, 2022Updated 3 years ago
- A fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools.☆45Feb 5, 2026Updated last month
- Development repo for pyani-plus (the next iteration of pyani)☆25Mar 11, 2026Updated last week
- Reorients assembled microbial sequences☆135Aug 21, 2025Updated 6 months ago
- BACTpipe: An assembly and annotation pipeline for bacterial genomics☆20Dec 3, 2024Updated last year
- Strain-level haplotyping for metagenomes with short or long-reads.☆65Apr 10, 2025Updated 11 months ago
- post processing of bacterial pangenome gene presence/absence matrices☆64Jan 19, 2026Updated 2 months ago
- A toolbox for pangenome analysis and threshold evaluation.☆100Jul 8, 2022Updated 3 years ago
- PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identifi…☆43Jul 23, 2021Updated 4 years ago
- ☆22Apr 3, 2023Updated 2 years ago
- (Meta-)genome screening for functional and natural product gene sequences☆103Updated this week
- ☆85Jan 16, 2026Updated 2 months ago
- A tool for the identification of coincident (associating and dissociating) genes in pangenomes.☆110Oct 20, 2023Updated 2 years ago
- Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.☆148Jan 9, 2026Updated 2 months ago
- A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome☆105Dec 5, 2025Updated 3 months ago
- Population analysis PIPEline 🛠🧬☆23Mar 2, 2026Updated 2 weeks ago
- scripts for microbiome analysis☆12Jul 25, 2024Updated last year
- Prediction of prophages from bacterial genomes☆81Feb 2, 2026Updated last month
- Colinear block visualisation tool☆31Jan 17, 2024Updated 2 years ago
- Bacterial Operon Finder for Functional Organization☆15Nov 14, 2023Updated 2 years ago
- Bacterial taxonomy construction and evaluation in R☆15Jan 30, 2024Updated 2 years ago
- alignment-free coverage calculation for metagenomic binning >100 times faster☆50Mar 13, 2025Updated last year
- MiGA: Microbial Genomes Atlas☆32Updated this week
- Assessing the quality of metagenome-derived genome bins using machine learning☆252Mar 20, 2025Updated last year
- A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concat…☆60Dec 5, 2025Updated 3 months ago
- Perform taxonomic profiling analyses for long-read shotgun metagenomic datasets. Developed for the Long Read Sequencing Workshop 2022 at …☆13May 12, 2022Updated 3 years ago