leaemiliepradier / PlasForestLinks
A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes
☆19Updated 2 years ago
Alternatives and similar repositories for PlasForest
Users that are interested in PlasForest are comparing it to the libraries listed below
Sorting:
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆26Updated 3 years ago
- A taxonomic classifier of plasmids☆27Updated 4 years ago
- A pipeline for bioinformatics analysis of bacterial genomes☆30Updated 2 weeks ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆49Updated last month
- Whole genome core alignments from multiple draft genomes☆13Updated 8 years ago
- ☆26Updated 2 years ago
- Calculate assocations between genes and traits☆25Updated 5 months ago
- Downstream processing of VAMB binning for Viral Elucidation☆51Updated last year
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆29Updated 2 years ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- plasmidVerify: plasmid contig verification tool☆13Updated 5 years ago
- ☆13Updated last year
- Plasmid exploration of bacterial genomes☆18Updated 3 years ago
- ☆19Updated 2 years ago
- Bacterial GWAS analysis☆43Updated last month
- MDMcleaner the assessment, classification and refinement tool for microbial dark matter SAGs and MAGs☆24Updated 2 years ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆36Updated 4 months ago
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆24Updated last year
- Classify metagenomic contigs as eukaryotic or prokaryotic☆39Updated 2 years ago
- Fast pairwise transmission inference from single genome and/or metagenomic data☆21Updated 3 weeks ago
- ☆13Updated 7 years ago
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆30Updated 10 months ago
- EzAAI - High Throughput Prokaryotic AAI Calculator☆44Updated 3 weeks ago
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated last year
- Order and orientation of complete bacterial genomes☆28Updated last month
- PlasX, a machine learning classifier for identifying plasmid sequences based on genetic architecture☆37Updated 3 years ago
- Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf☆50Updated last year
- SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…☆34Updated 2 years ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Updated 6 years ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆60Updated 2 months ago