55 docs tagged with "bacteria"

Mass screening of contigs for antimicrobial and virulence genes.

Mass screening of contigs for antimicrobial and virulence genes.

Summarize Abricate screening results.

Identify antimicrobial resistance genes using AMRFinderPlus.

Detect antimicrobial resistance and virulence genes.

Determine the agr locus type and operon variants in Staphylococcus aureus.

Find antimicrobial resistance genes and point mutations.

Identify antimicrobial resistance and virulence genes in gene or protein sequences.

Download and index the latest AMRFinder+ database.

Rapidly identify genes by creating local assemblies from paired-end reads.

Download and prepare reference databases for ARIBA analysis.

Assemble bacterial genomes using short read, long read, or hybrid strategies.

Assemble bacterial genomes using automated assembler selection.

Create genomic sketches and perform rapid taxonomic classification.

Predict genome size and route samples based on taxonomic classification.

Rapid bacterial genome annotation.

Download the Bakta annotation database.

Rapid and standardized annotation of bacterial genomes and plasmids.

In silico typing and characterization of *Bacillus cereus* group genomes.

Assess genome quality using lineage-specific marker sets.

Assess genome quality using machine learning.

Determine the phylogroup of Escherichia coli isolates.

Inference of recombination in bacterial genomes.

Systematically search for anti-phage defense systems.

Detect anti-phage defense systems using HMM profiles.

Download and package the DefenseFinder and CasFinder model databases.

Predict *Escherichia coli* serotype (O and H antigens).

*emm*-typing of *Streptococcus pyogenes* (Group A Strep) assemblies.

Parse Mykrobe results to genotype *Salmonella* Typhi.

Taxonomic classification of bacterial and archaeal genomes using GTDB-Tk.

Download and configure the GTDB-Tk reference database.

Detect recombination and construct a recombination-free phylogeny.

Predict *Haemophilus influenzae* capsule serotype.

Predict *Haemophilus parasuis* serotype.

Identify insertion sites and orientation of mobile genetic elements.

Genotyping and screening of *Klebsiella* genome assemblies.

In silico Sequence Based Typing (SBT) of *Legionella pneumophila*.

Predict *Listeria monocytogenes* serogroup.

Detect sequence variations in the *mcr-1* colistin resistance gene.

Serotyping and finetyping of *Neisseria meningitidis*.

Automatic Multi-Locus Sequence Typing (MLST) of genome assemblies.

Determine multilocus sequence types (MLST) from bacterial assemblies.

Reconstruct and type plasmids from a bacterial genome assembly.

Predict antibiotic resistance from sequence reads.

Serotyping and Multi-Antigen Sequence Typing (MAST) of *Neisseria gonorrhoeae*.

Download the nohuman database for human read removal.

Predict O-antigen serogroup of Pseudomonas aeruginosa isolates.

Predict Penicillin Binding Protein (PBP) type of *Streptococcus pneumoniae* assemblies.

Annotate prokaryotic genomes.

Annotate bacterial genomes with functional information.

Predict antimicrobial resistance from protein or nucleotide data.

Rapid large-scale prokaryote pan genome analysis.

Pan-genome wide association studies.

Core-SNP alignment from Snippy outputs.

Rapid haploid variant calling and core genome alignment.