Rapid determination of appropriate reference genomes.
☆100Jan 22, 2025Updated last year
Alternatives and similar repositories for referenceseeker
Users that are interested in referenceseeker are comparing it to the libraries listed below
Sorting:
- Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.☆121Jan 22, 2025Updated last year
- A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences☆63Nov 20, 2025Updated 3 months ago
- Reorients assembled microbial sequences☆133Aug 21, 2025Updated 6 months ago
- Create a tree using Mash distances☆182Oct 24, 2023Updated 2 years ago
- Rapid & standardized annotation of bacterial genomes, MAGs & plasmids☆607Feb 18, 2026Updated 2 weeks ago
- A tool for removing redundant genomes from a set of assemblies☆79Sep 10, 2025Updated 5 months ago
- A toolbox for pangenome analysis and threshold evaluation.☆99Jul 8, 2022Updated 3 years ago
- Targeted Detection and Reconstruction of Plasmids☆22May 7, 2024Updated last year
- Assemble bacterial isolate genomes from Nanopore reads☆128Jan 22, 2025Updated last year
- A scalable bacterial genome assembly, annotation and analysis pipeline☆74Dec 5, 2023Updated 2 years ago
- A tool for generating consensus long-read assemblies for bacterial genomes☆220Feb 23, 2026Updated last week
- A pipeline for running AMRfinderPlus and collating results into functional classes☆91Dec 3, 2025Updated 3 months ago
- A hybrid assembly and MAG recovery pipeline (and more!)☆104Jan 27, 2026Updated last month
- Python package for detection of chimerism and contamination in prokaryotic genomes.☆81Nov 23, 2023Updated 2 years ago
- a collection of scripts for organising bacterial genomes by species☆81Mar 18, 2022Updated 3 years ago
- Intra-species bacterial contamination detection☆25Feb 5, 2026Updated last month
- Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.☆236Oct 12, 2025Updated 4 months ago
- Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.☆105Jan 22, 2026Updated last month
- geNomad: Identification of mobile genetic elements☆291Nov 10, 2025Updated 3 months ago
- An updated pipeline for pangenome investigation☆345Jan 15, 2026Updated last month
- High-quality Nanopore-only genome polisher☆69Aug 16, 2024Updated last year
- TAXnomic Profile Aggregation and STAndardisation☆42Nov 18, 2025Updated 3 months ago
- Predict plasmids from uncorrected long read data☆41Oct 31, 2025Updated 4 months ago
- CFSAN Shigella Typing Pipeline☆15Jul 6, 2023Updated 2 years ago
- genome_updater is a bash script that downloads and updates (non-redundant) snapshots of the NCBI Genomes repository (RefSeq/GenBank) with…☆166Feb 11, 2026Updated 3 weeks ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆49Jan 14, 2026Updated last month
- Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.☆186Feb 24, 2026Updated last week
- A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.☆35Dec 2, 2024Updated last year
- Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.☆148Jan 9, 2026Updated last month
- a short-read polishing tool for long-read assemblies☆207Sep 19, 2025Updated 5 months ago
- zDB: comparative bacterial genomics made easy☆38Feb 2, 2026Updated last month
- Bacterial Annotation by Learned Representation of Genes☆60Jan 22, 2021Updated 5 years ago
- Finding regions of similarity between plasmids☆17Nov 2, 2022Updated 3 years ago
- Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf☆50Apr 16, 2024Updated last year
- Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure☆173Feb 26, 2026Updated last week
- Order and orientation of complete bacterial genomes☆29Jul 11, 2025Updated 7 months ago
- Genome size estimation from long read overlaps☆81Updated this week
- ⚡️🧬 FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies☆25Nov 19, 2025Updated 3 months ago
- interactive barplot for amplicon sequencing☆13Dec 5, 2024Updated last year