ukhsa-collaboration / LOMALinks
A Nextflow pipeline designed to classify, align and assemble nanopore metagenomic reads.
☆13Updated 2 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 3 months ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆25Updated 2 years ago
- Nanomotif - a tool for identifying methylated motifs in metagenomic samples☆27Updated last month
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- Extracts contigs harbouring a target gene / sequence from assemblies and aligns the contigs around the target sequence☆13Updated 7 years ago
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆22Updated 2 years ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆20Updated 6 years ago
- Calculate assocations between genes and traits☆23Updated 2 months ago
- Genome size estimation from long read overlaps☆56Updated last month
- Automatic evaluation of HGTs☆29Updated 4 months ago
- Mobile Genetic Elements Retrieving Tool☆15Updated last week
- Automated strain separation of low-complexity metagenomes☆51Updated 3 years ago
- pGWAS and functional filtering pipeline to identify candidate adaptive genetic traits in bacteria☆11Updated 7 years ago
- Recombination-free trees☆58Updated 2 months ago
- Long read metagenomics practical at EBAME18☆18Updated 6 years ago
- Predict MLST directly from uncorrected long reads☆27Updated 3 years ago
- whole genome MLST analysis☆43Updated 2 months ago
- Bacterial GWAS analysis☆40Updated last week
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆27Updated 7 months ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆25Updated 8 months ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆28Updated last year
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆36Updated 2 months ago
- Plasmid analysis using rearrangement distances☆42Updated last week
- Gene Absence Presence Identification tool.☆26Updated 2 months ago
- ☆36Updated 3 years ago
- Plasmid exploration of bacterial genomes☆18Updated 3 years ago
- Quality control plotting for long reads☆10Updated last year
- SISTR (Salmonella In Silico Typing Resource) command-line tool☆28Updated last month
- ☆20Updated 9 months ago