genomicepidemiology / ARGprofiler
A pipeline for for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets
☆25Updated 2 weeks ago
Alternatives and similar repositories for ARGprofiler:
Users that are interested in ARGprofiler are comparing it to the libraries listed below
- ☆48Updated 9 months ago
- Growth Rate Index (GRiD) measures bacterial growth rate from reference genomes (including draft quality genomes) and metagenomic bins at …☆32Updated 4 years ago
- zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)☆52Updated last month
- Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf☆48Updated 9 months ago
- This is a comprehensive database for fast and accurately analyzing the phosphorus cycling genes.☆31Updated 2 years ago
- Improvement of metagenome-assembled genomes☆51Updated 4 years ago
- PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.☆58Updated last year
- AMR++ is a bioinformatic pipeline meant to aid in the analysis of raw sequencing reads to characterize the profile of antimicrobial resis…☆31Updated 2 months ago
- ☆18Updated 4 months ago
- This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria.☆20Updated last year
- ☆62Updated last month
- MaAsLin3: Microbiome Multivariate Association with Linear Models☆24Updated 2 weeks ago
- PlasX, a machine learning classifier for identifying plasmid sequences based on genetic architecture☆32Updated 2 years ago
- Collection of notebooks describing the basic analysis workflow for a 16S rRNA gene amplicon sequencing project☆11Updated 2 years ago
- EzAAI - High Throughput Prokaryotic AAI Calculator☆37Updated 3 months ago
- Prophage Activity Estimator☆26Updated 8 months ago
- Downstream processing of VAMB binning for Viral Elucidation☆47Updated 6 months ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆34Updated last week
- whole genome MLST analysis☆40Updated 8 months ago
- ☆41Updated 3 years ago
- A pipeline for the macro- and micro-diversity analyses and visualization of metagenomic-derived populations☆40Updated last year
- Calculation of the Percentage of Conserved Proteins following Qin, Xie et al. 2014 but using DIAMOND instead of BLASTP for alignments.☆23Updated 3 months ago
- SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…☆31Updated last year
- Pipeline for Reproducible and Scalable Integration of Metagenomic and Metatranscriptomic Data☆14Updated this week
- Discover and annotate the virome☆35Updated 3 months ago
- A toolkit for prokaryotic comparative genomics☆40Updated last week
- MAG Circularization Method☆33Updated 2 years ago
- ☆15Updated last month
- PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples☆45Updated last year
- Gene Absence Presence Identification tool.☆26Updated last year