leaemiliepradier / PlasForest
A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes
☆18Updated 2 years ago
Alternatives and similar repositories for PlasForest:
Users that are interested in PlasForest are comparing it to the libraries listed below
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆25Updated 2 years ago
- Calculate assocations between genes and traits☆23Updated last month
- plasmidVerify: plasmid contig verification tool☆13Updated 5 years ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆28Updated last year
- ☆25Updated last year
- ☆13Updated 7 years ago
- A pipeline for bioinformatics analysis of bacterial genomes☆28Updated this week
- SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…☆31Updated 2 years ago
- Plasmid exploration of bacterial genomes☆18Updated 3 years ago
- ☆20Updated 8 months ago
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆23Updated 9 months ago
- Fast pairwise transmission inference from single genome and/or metagenomic data☆21Updated 7 months ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆20Updated 6 years ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆27Updated 6 months ago
- Prophage Activity Estimator☆26Updated 11 months ago
- MDMcleaner the assessment, classification and refinement tool for microbial dark matter SAGs and MAGs☆24Updated 2 years ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆44Updated last week
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆35Updated last week
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆21Updated 2 years ago
- Structural and functional annotation of eukaryotic metagenome-assembled genomes☆22Updated last year
- This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria.☆20Updated last year
- Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf☆48Updated last year
- PlasX, a machine learning classifier for identifying plasmid sequences based on genetic architecture☆34Updated 3 years ago
- MAG Circularization Method☆33Updated 2 years ago
- Identify and remove contaminants from metagenome-assembled genomes☆18Updated last year
- Strain-level haplotyping for metagenomes with short or long-reads.☆51Updated 3 weeks ago
- Downstream processing of VAMB binning for Viral Elucidation☆49Updated 10 months ago
- Gene Absence Presence Identification tool.☆26Updated last month
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆26Updated 5 years ago