A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes
☆23Apr 20, 2023Updated 3 years ago
Alternatives and similar repositories for PlasForest
Users that are interested in PlasForest are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Plasmid exploration of bacterial genomes☆27Mar 2, 2022Updated 4 years ago
- A tool to classify sequences of plasmid or chromosomal origin. A paper describing this tool is available at: https://journals.plos.org/pl…☆34Jun 17, 2024Updated 2 years ago
- PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identifi…☆44Jul 23, 2021Updated 5 years ago
- Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf☆50Updated this week
- Plascad is a computationally efficient tool designed for plasmids classification, antibiotic resistance genes (ARGs) annotation and plasm…☆52Feb 2, 2021Updated 5 years ago
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- Small utility script to submit genomes to PHASTER for phage detection☆26Oct 21, 2021Updated 4 years ago
- DeepSig - Predictor of signal peptides in proteins based on deep learning☆31Mar 25, 2023Updated 3 years ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆36Feb 3, 2021Updated 5 years ago
- ☆38Apr 15, 2024Updated 2 years ago
- SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…☆38Feb 26, 2023Updated 3 years ago
- A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates☆15Aug 26, 2024Updated 2 years ago
- ☆22Oct 4, 2023Updated 2 years ago
- Software for prediction of plasmid sequences in metagenomic assemblies☆111Jun 28, 2021Updated 5 years ago
- hAMRoaster is an analysis pipeline that can compare the output of tools for detecting AMR genes and provide metrics of their performance☆23Mar 8, 2024Updated 2 years ago
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- ⚡️🧬 FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies☆26Jul 10, 2026Updated last month
- Predict plasmids from uncorrected long read data☆41Feb 27, 2026Updated 6 months ago
- zDB: comparative bacterial genomics made easy☆42Updated this week
- Pipeline detecting distant and putative novel insertion sequences in prokaryotic genomes☆13Jun 10, 2021Updated 5 years ago
- ☆30Aug 2, 2026Updated last month
- A pipeline for running AMRfinderPlus and collating results into functional classes☆102Aug 30, 2026Updated last week
- Download assembly files from NCBI☆12May 9, 2023Updated 3 years ago
- Wrapper for short and long read mapping, creation of quality report(s) and estimation of genome size☆12Sep 30, 2025Updated 11 months ago
- Plasmid and antimicrobial resistance pipeline☆16Apr 30, 2026Updated 4 months ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies☆183Apr 16, 2025Updated last year
- ☆38Nov 11, 2022Updated 3 years ago
- Easy-to-use web application for visualization and comparison of genomes in Genbank file☆22May 27, 2022Updated 4 years ago
- This repository contains R code for building a heatmap and histogram with the output of FastANI☆18Sep 14, 2021Updated 4 years ago
- Bioinformatics tool to find integrons in bacterial genomes☆94May 7, 2025Updated last year
- An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features.☆50Apr 20, 2023Updated 3 years ago
- A pipeline for bioinformatics analysis of bacterial genomes☆34Jul 17, 2026Updated last month
- An updated pipeline for pangenome investigation☆375Jul 2, 2026Updated 2 months ago
- Genome-wide gene gain/loss mapping tool using DTL(Duplication-Transfer-Loss) reconciliation method☆18Dec 29, 2022Updated 3 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- A taxonomic classifier of plasmids☆29Jul 7, 2021Updated 5 years ago
- Neural Bacteriocin Identifier - a recurrent neural network based software to predict bacteriocins from protein sequences.☆18Mar 25, 2023Updated 3 years ago
- Prediction of prophages from bacterial genomes☆88May 1, 2026Updated 4 months ago
- Circular bacterial genome plots based on BLAST or NUCMER/PROMER alignments☆110Dec 11, 2023Updated 2 years ago
- IslandPath standalone software☆38Nov 7, 2023Updated 2 years ago
- High-quality Nanopore-only genome polisher☆71Aug 16, 2024Updated 2 years ago
- plasmidVerify: plasmid contig verification tool☆15Apr 30, 2020Updated 6 years ago