metagenlab / assembly_finderView external linksLinks
snakemake-powered cli to download genomes using NCBI datasets
☆14Aug 14, 2025Updated 6 months ago
Alternatives and similar repositories for assembly_finder
Users that are interested in assembly_finder are comparing it to the libraries listed below
Sorting:
- ☆10Jun 9, 2025Updated 8 months ago
- zDB: comparative bacterial genomics made easy☆38Feb 2, 2026Updated last week
- Snakemake pipeline for simulating shotgun metagenomic samples☆29Sep 4, 2025Updated 5 months ago
- software to identify primers that can distinguish genomes☆20Jan 23, 2026Updated 3 weeks ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆35Apr 26, 2025Updated 9 months ago
- A repo with just adapter sequences☆15Jul 7, 2025Updated 7 months ago
- ☆25Updated this week
- whole genome MLST analysis☆51Jun 13, 2025Updated 8 months ago
- Dryad is a Nextflow pipeline for examining prokaryote relatedness. Dryad can perform a reference free analysis and/or SNP analysis.☆18Nov 20, 2025Updated 2 months ago
- Finding regions of similarity between plasmids☆17Nov 2, 2022Updated 3 years ago
- A streamlined workflow and GUI for real-time species identification and pathogen characterization via nanopore sequencing data. Engineere…☆20Oct 4, 2024Updated last year
- Genome size estimation from long read overlaps☆80Dec 1, 2025Updated 2 months ago
- Targeted Detection and Reconstruction of Plasmids☆22May 7, 2024Updated last year
- Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.☆13Dec 24, 2025Updated last month
- rapid serotyping of Vibrio parahaemolyticus from whole genome sequencing data using serogroup-specific genes☆10Sep 2, 2021Updated 4 years ago
- TAXnomic Profile Aggregation and STAndardisation☆41Nov 18, 2025Updated 2 months ago
- Pipeline for analyzing rare mutations in metagenome-assembled genomes☆10Apr 4, 2025Updated 10 months ago
- BRICK creates a BRIG-like interactive data visualisation for bacterial genome annotations and comparisons☆21Dec 9, 2025Updated 2 months ago
- Calculate confidence scores from Kraken2 output☆23Feb 18, 2024Updated last year
- An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features.☆49Apr 20, 2023Updated 2 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
- Hybrid Assembler for Plasmids☆10Jul 28, 2022Updated 3 years ago
- Iterative Gene clUster Analysis, a high-throughput method for gene cluster family identification.☆17Jan 31, 2026Updated last week
- ☆14Feb 10, 2025Updated last year
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆24Feb 6, 2023Updated 3 years ago
- A taxonomic classifier of plasmids☆28Jul 7, 2021Updated 4 years ago
- Remove human reads from a sequencing run☆47Dec 16, 2025Updated last month
- A k-mer search engine for all Sequence Read Archive public accessions☆36Oct 29, 2024Updated last year
- ☆25Jan 30, 2025Updated last year
- Generate basic stats for an assembly.☆13Feb 12, 2023Updated 3 years ago
- A tooL for Prokaryotic Phylogeny And Clustering Analysis☆13Jul 28, 2025Updated 6 months ago
- Taxonomy classification of viral sequences / contigs☆12Jul 15, 2025Updated 6 months ago
- Development repo for pyani-plus (the next iteration of pyani)☆24Jan 26, 2026Updated 2 weeks ago
- Prokaryotic Pangenome Analysis☆24Dec 3, 2021Updated 4 years ago
- PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.☆29Aug 20, 2025Updated 5 months ago
- RabbitTClust: enabling fast clustering analysis of millions bacteria genomes with MinHash sketches☆53Feb 4, 2026Updated last week
- A pipeline for bioinformatics analysis of bacterial genomes☆32Updated this week
- ☆26Aug 2, 2023Updated 2 years ago
- Phylotype your strains using Clermont's 2013 method: ezclermont.org☆15Aug 5, 2022Updated 3 years ago