labgem / PlaScope
Plasmid exploration of bacterial genomes
☆17Updated 2 years ago
Related projects: ⓘ
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆24Updated 2 years ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and met…☆38Updated last week
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆18Updated 5 years ago
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆17Updated last year
- Predict MLST directly from uncorrected long reads☆25Updated 2 years ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 3 years ago
- Archived - please see updated sccmec tool at link below☆13Updated 3 weeks ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆21Updated 3 weeks ago
- Colinear block visualisation tool☆30Updated 8 months ago
- ☆24Updated this week
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆27Updated last year
- ☆29Updated 9 months ago
- 🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files☆23Updated 6 years ago
- Recombination-free trees☆55Updated last year
- PlasX, a machine learning classifier for identifying plasmid sequences based on genetic architecture☆28Updated 2 years ago
- SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…☆29Updated last year
- viralFlye pipeline☆18Updated last month
- Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf☆44Updated 5 months ago
- Bacterial taxonomy construction and evaluation in R☆12Updated 7 months ago
- CFSAN Shigella Typing Pipeline☆14Updated last year
- ☆10Updated 4 years ago
- Predict plasmids from uncorrected long read data☆39Updated 4 years ago
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆24Updated 5 months ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆22Updated 4 months ago
- Structural and functional annotation of eukaryotic metagenome-assembled genomes☆21Updated last year
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆25Updated last month
- Calculate assocations between genes and traits☆18Updated 2 months ago
- Standalone Python re-implementation of the POLCA polisher from MaSuRCA☆25Updated 3 weeks ago
- Identify phage regions in bacterial genomes for masking purposes☆30Updated 5 years ago
- plasmidVerify: plasmid contig verification tool☆12Updated 4 years ago