67 docs tagged with "bactopia-tool"

Mass screening of contigs for antimicrobial resistance and virulence genes.

A NATA accredited tool for reporting the presence of antimicrobial resistance genes.

Rapid identification of Staphylococcus aureus agr locus type and agr operon variants.

Bactopia Tool: Amrfinderplus.

Gene identification through local assemblies.

Rapid annotation of bacterial genomes and plasmids.

Search against nucleotide BLAST databases using nucleotide queries.

Search against protein BLAST databases using protein queries.

Search against protein BLAST databases using translated nucleotide queries.

Estimate taxonomic abundance of metagenomic samples.

Taxonomic classification of Bacillus cereus group isolates.

Assessment of genome assembly completeness using evolutionarily informed expectations.

Assessment of microbial genome assembly quality.

Machine learning-based assessment of microbial genome assembly quality.

In silico phylotyping of Escherichia genus.

Systematic identification of anti-phage defense systems.

In silico prediction of Escherichia coli serotype.

Functional annotation of proteins using orthologous groups and phylogenies.

emm-typing of Streptococcus pyogenes assemblies.

Fast alignment-free computation of whole-genome Average Nucleotide Identity.

Identification, classification, and annotation of translated gene matches.

Salmonella Typhi genotyping with lineage assignment.

Run all available MLST schemes for a species against an assembly

Identify marker genes and assign taxonomic classifications using GTDB.

Identify cap locus serotype and structure in Haemophilus influenzae assemblies.

Serotype prediction of Haemophilus parasuis assemblies.

Identify insertion sequence positions in bacterial genomes.

Comprehensive screening of Klebsiella genomes for virulence and resistance determinants.

Taxonomic classification of metagenomic sequence reads.

Sequence Based Typing (SBT) of Legionella pneumophila.

Serogroup typing prediction for Listeria monocytogenes.

Calculate Mash distances between sequences and reference genomes.

Rapid phylogenetic tree construction using Mash distances.

Sequence variation analysis of mcr-1 genes (mobilized colistin resistance).

Comprehensive typing of Neisseria meningitidis.

MinMER-assisted species-specific tool selection and execution.

Estimate species abundances from metagenomic samples.

Automatic Multi-Locus Sequence Type (MLST) calling from assembled contigs.

Reconstruction and annotation of plasmids from bacterial genome assemblies.

Antimicrobial resistance detection for specific bacterial species.

Multi-antigen sequence typing of Neisseria gonorrhoeae.

Pangenome analysis with optional core-genome phylogeny.

In silico serogrouping of Pseudomonas aeruginosa isolates.

Penicillin Binding Protein (PBP) typing for Streptococcus pneumoniae.

Prediction of prophages in bacterial and archaeal genomes.

Bactopia Tool: Plasmidfinder.

Capsular type assignment to Streptococcus pneumoniae from sequence reads.

Rapid whole genome annotation of bacterial, archaeal, and viral genomes.

Quality assessment of assembled contigs using QUAST.

Prediction of antibiotic resistance genes using RGI.

Typing of SCCmec cassettes in Staphylococcus aureus assemblies.

Removal of human and contaminant sequences from metagenomic reads.

Salmonella serotype prediction from sequencing reads or assemblies.

Serotyping of Streptococcus pneumoniae from Illumina paired-end reads.

Prediction of Shigella serotypes and differentiation from EIEC.

Rapid determination of Shigella serotypes from sequencing reads.

In silico serotype prediction for Shigella and Enteroinvasive E. coli (EIEC).

Serovar prediction of Salmonella enterica from assemblies.

Rapid haplotype variant calling and core genome alignment.

spa typing of Staphylococcus aureus assemblies.

Serotype prediction of Streptococcus suis assemblies.

Comprehensive typing of Staphylococcus aureus genomes.

Serotype identification of Shiga toxin-producing E. coli.

Taxonomic profiling by abundance-corrected MinHash.

Search against translated nucleotide databases using protein queries.

Search against translated nucleotide databases using translated nucleotide queries.

Detection of antimicrobial resistance and lineage typing of Mycobacterium tuberculosis.