ukhsa-collaboration / LOMALinks
A Nextflow pipeline designed to classify, align and assemble nanopore metagenomic reads.
☆14Updated 3 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 …☆13Updated 3 years ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆59Updated last week
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- Nanomotif - a tool for identifying methylated motifs in metagenomic samples☆27Updated last week
- Mobile Genetic Elements Retrieving Tool☆15Updated last month
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆28Updated 8 months ago
- Predict plasmids from uncorrected long read data☆40Updated 5 years ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆25Updated 2 years ago
- Automatic evaluation of HGTs☆29Updated 4 months ago
- Recombination-free trees☆58Updated 3 months ago
- reference-based long read assemblies of bacterial genomes☆49Updated 3 years ago
- Genome size estimation from long read overlaps☆57Updated 2 months ago
- Lightweight bioinformatics pipeline for microbial genome recovery☆10Updated 4 months ago
- Long read metagenomics practical at EBAME18☆18Updated 6 years ago
- whole genome MLST analysis☆43Updated 2 weeks ago
- 🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files☆24Updated 7 years ago
- Gene Absence Presence Identification tool.☆26Updated 2 months ago
- CFSAN Shigella Typing Pipeline☆14Updated last year
- ☆20Updated 9 months ago
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆36Updated 3 months ago
- pGWAS and functional filtering pipeline to identify candidate adaptive genetic traits in bacteria☆11Updated 7 years ago
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆22Updated 3 years ago
- A MinION-based pipeline for tracking species biodiversity☆13Updated last year
- Extracts contigs harbouring a target gene / sequence from assemblies and aligns the contigs around the target sequence☆13Updated 7 years ago
- ☆36Updated 3 years ago
- Automated strain separation of low-complexity metagenomes☆51Updated 3 years ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆20Updated 6 years ago
- PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.☆58Updated last year
- Snakemake workflow for bacterial genome assembly + polishing for Oxford Nanopore (ONT) sequencing using multiple tools.☆27Updated last year
- Quality control plotting for long reads☆10Updated last year