bhattlab / MGEfinderLinks
A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
☆124Updated 2 years ago
Alternatives and similar repositories for MGEfinder
Users that are interested in MGEfinder are comparing it to the libraries listed below
Sorting:
- A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome☆100Updated 3 weeks ago
- Recovery of prokaryotic genomes from shotgun metagenomic sequencing data☆62Updated 4 years ago
- Horizontal gene transfer (HGT) identification pipeline☆65Updated 2 years ago
- Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.☆146Updated last week
- Insertion sequences (Insertion Element) [https://en.wikipedia.org/wiki/Insertion_sequence] collected from ISfinder (https://isfinder.biot…☆72Updated 5 years ago
- A wrapper to identify, bin, classify, and predict host-viral relationship for viruses☆83Updated last year
- A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during…☆82Updated 3 months ago
- phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.☆88Updated 2 years ago
- Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets☆75Updated last year
- HGTector2: Genome-wide prediction of horizontal gene transfer based on distribution of sequence homology patterns.☆142Updated 2 years ago
- A toolbox for comparative genomics.☆107Updated 4 years ago
- Contains a fasta format database of a large variety of mobile genetic elements and an annotation file☆52Updated 4 years ago
- DDBJ Fast Annotation and Submission Tool☆83Updated 3 months ago
- Supporting code for uncultivated gut virus manuscript☆77Updated 2 years ago
- All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")☆80Updated 2 years ago
- A pipeline for nanopore long-read metagenomic analysis.☆52Updated last month
- Find endogenous viral elements in genomes☆21Updated 3 months ago
- ☆152Updated last year
- DAS Tool☆163Updated last year
- Pipeline for metabolic annotation of microbial genomes☆150Updated 9 months ago
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆118Updated last year
- An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features.☆49Updated 2 years ago
- VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies☆145Updated 2 weeks ago
- Development version of Easyfig☆102Updated 2 years ago
- Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can b…☆148Updated 2 months ago
- Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.☆230Updated 2 months ago
- A tool for generating consensus long-read assemblies for bacterial genomes☆207Updated 2 months ago
- Assembly methods for nanopore-based metagenomic sequencing: a comparative study☆18Updated 5 years ago
- Bioinformatics tool to find integrons in bacterial genomes☆83Updated 7 months ago
- A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing☆69Updated 4 years ago