ukhsa-collaboration / LOMAView external linksLinks
A Nextflow pipeline designed to classify, align and assemble nanopore metagenomic reads.
☆17Mar 18, 2025Updated 10 months ago
Alternatives and similar repositories for LOMA
Users that are interested in LOMA are comparing it to the libraries listed below
Sorting:
- 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
- ☆11Nov 13, 2025Updated 3 months ago
- ☆15May 22, 2025Updated 8 months ago
- screening metagenomes for arbitrary lineages, using gene-centric assembly methods and phylogenetics☆11Oct 29, 2020Updated 5 years ago
- A nextflow version of the Wochenende reference metagenome binning and visualization pipeline☆15Dec 14, 2024Updated last year
- Extracts contigs harbouring a target gene / sequence from assemblies and aligns the contigs around the target sequence☆13May 15, 2018Updated 7 years ago
- Genome-wide gene gain/loss mapping tool using DTL(Duplication-Transfer-Loss) reconciliation method☆17Dec 29, 2022Updated 3 years ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆33Dec 4, 2025Updated 2 months ago
- ccfind - circular complete genome finder with clues of terminal redundancy☆16Updated this week
- A bacterial GWAS pipeline written in Nextflow that uses Pyseer; Part III Project for Systems Biology at the University of Cambridge☆21Jan 20, 2026Updated 3 weeks ago
- Small pipeline to cluster viral genomes based on their k-mer content. WiP☆18Feb 3, 2026Updated last week
- CFSAN Shigella Typing Pipeline☆15Jul 6, 2023Updated 2 years ago
- Real-time analysis pipeline for nanopore 16S rRNA data☆15Nov 29, 2022Updated 3 years ago
- ProkEvo - an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses.☆18Aug 16, 2021Updated 4 years ago
- Sequence-independent identification and removal of adapters/systemic contamination in shotgun sequencing data. https://doi.org/10.1093/bi…☆18Apr 4, 2023Updated 2 years ago
- ViralCC: leveraging metagenomic proximity-ligation to retrieve complete viral genomes☆18Feb 3, 2026Updated last week
- Bacterial genomes finishing tool for structural insights on draft genomes☆23Sep 22, 2023Updated 2 years ago
- aweMAGs: a fully automated workflow for eukariotic MAGs☆20Jun 6, 2023Updated 2 years ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Feb 15, 2019Updated 7 years ago
- compare sequences to a shared root reference sequence.☆24Oct 19, 2021Updated 4 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
- Add new taxa or taxonomic groups to the NCBI Taxdump files☆20Mar 9, 2020Updated 5 years ago
- ☆22Apr 20, 2023Updated 2 years ago
- Frequently used commands in Bioinformatics☆23Updated this week
- Finding prophage regions in bacterial genomes using brute force☆22Jan 20, 2023Updated 3 years ago
- An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and…☆51Jul 24, 2025Updated 6 months ago
- kASA - k-Mer Analysis of Sequences based on Amino acid-like encoding☆23Aug 23, 2023Updated 2 years ago
- Repeat and haplotype aware error correction in nanopore sequencing reads with DeChat☆25May 10, 2025Updated 9 months ago
- ⚡️🧬 FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies☆26Nov 19, 2025Updated 2 months ago
- ARG normalization by mapping to the ARO ontology.☆62Jul 30, 2025Updated 6 months ago
- Metagenomic Analysis in Real Time☆29Nov 18, 2025Updated 2 months ago
- Bacterial analysis toolbox for full ESKAPE pathogen characterization and profiling the resistome, mobilome, virulome & phylogenomics usin…☆26Jan 30, 2025Updated last year
- Better and faster Rust implementation of the FragGeneScan gene prediction model for short and error-prone reads.☆30Feb 3, 2026Updated last week
- Identify short variants and structural variants from raw sequencing data or genomic sequences☆34Mar 27, 2024Updated last year
- UPHL's Reference Free Pipeline☆27Oct 30, 2025Updated 3 months ago
- 🚦🧬 Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs☆68Sep 26, 2024Updated last year
- Read contamination removal☆25Jan 24, 2024Updated 2 years ago
- Recombination-free trees☆63Sep 1, 2025Updated 5 months ago
- Microbial agile accurate SNP Typer☆30Dec 27, 2023Updated 2 years ago