Making whole bacterial genome sequencing data analysis easy
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Updated
Mar 13, 2023 - Shell
Making whole bacterial genome sequencing data analysis easy
Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure
Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
Code for the paper "Antimicrobial resistance prediction in clinical isolates through machine learning on MALDI-TOF mass spectra"
Harmonization of AMR predictor tool outputs
HydrAMP: a deep generative model for antimicrobial peptide discovery
AMR/VF LGT focused bacterial genomics analysis workflow
Antimicrobial resistance prediction app for KBase
Detect the presence of specific resistance genes in a sample using the IRIDA system
An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences
Scripts for ARIBA-based gene detection
PRAWNS: A fast and scalable bioinformatics tool that generates an efficient pan-genome representation of closely related whole genomes to provide a concise list of genomic features
MTB++ a software developed to predict antimicrobial resistance to 13 antibiotics and 3 families of antimicrobials.
Antimicrobial Resistance Test Interpretation Engine
Proof-of-concept for storing and querying harmonized AMR Genomic Analysis Results in datahike
Chromosomal mutations associated with nitrofurantoin resistance in Escherichia coli
Pipelines creating allelic presence-absence matrices from SRST2 and ARIBA results
Python code to integrate results of tb-pipeline and provide an antibiogram, mutations and variants
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