147 docs tagged with "sample-scope"

Mass screening of contigs for antimicrobial and virulence genes.

Mass screening of contigs for antimicrobial and virulence genes.

Identify antimicrobial resistance genes using AMRFinderPlus.

Detect antimicrobial resistance and virulence genes.

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

Identify Staphylococcus aureus agr locus type and operon variants.

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.

Identify genes by local assembly of reads.

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

Assemble bacterial genomes using automated assembler selection.

Search, validate, gather, or simulate input samples.

Search, validate, gather, and standardize input samples.

Automated quality control, error correction, and read subsampling.

Perform comprehensive quality control on sequencing reads.

Create genomic sketches and perform rapid taxonomic classification.

Create genomic sketches and perform rapid taxonomic classification.

Predict genome size and route samples based on taxonomic classification.

Rapid bacterial genome annotation.

Rapid and standardized annotation of bacterial genomes and plasmids.

Search a nucleotide database using a nucleotide query.

Search a protein database using a protein query.

Search a protein database using a translated nucleotide query.

Search a translated nucleotide database using a protein query.

Search a translated nucleotide database using a translated nucleotide query.

Search a nucleotide database using nucleotide query sequences.

Search protein sequences against protein database.

Translate nucleotide sequences and search protein database.

Taxonomic classification and abundance estimation.

Estimate species abundance from metagenomic reads.

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

In silico taxonomic classification of Bacillus cereus group genomes.

Assess genome assembly completeness using single-copy orthologs.

Assess genome assembly completeness using BUSCO.

Assess metagenome bin completeness using CheckM.

Assess genome quality using lineage-specific marker sets.

Assess metagenome bin completeness using CheckM2.

Download the pre-trained CheckM2 database.

Assess genome quality using machine learning.

Determine the phylogroup of Escherichia coli isolates.

Predict phylogroups of Escherichia coli from genome assemblies.

Systematically search for anti-phage defense systems.

Detect anti-phage defense systems using HMM profiles.

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

In silico prediction of Escherichia coli serotype.

Functional annotation through orthology assignment.

Download the eggNOG database for functional annotation.

Functional annotation of proteins using eggNOG orthology data.

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

Predict emm types of Streptococcus pyogenes from genome assemblies.

Identification, classification, and annotation of translated gene matches.

Gene Allele Mutation Microbial Assessment.

Assign genotypes to Salmonella Typhi genomes.

Parse Mykrobe results to genotype *Salmonella* Typhi.

Run all available MLST schemes for a species against an assembly

Run all available MLST schemes for a species against an assembly

Taxonomic classification with the Genome Taxonomy Database.

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

Download and configure the GTDB-Tk reference database.

Predict *Haemophilus influenzae* capsule serotype.

In silico serotyping of the Haemophilus influenzae capsule locus.

Predict *Haemophilus parasuis* serotype.

Rapid Haemophilus parasuis serotyping.

Identify insertion sites and orientation of mobile genetic elements.

Identify transposase insertion sites in bacterial genomes.

Genotyping and screening of *Klebsiella* genome assemblies.

Genotyping tool for Klebsiella pneumoniae and its related species complex.

Taxonomic classification and host filtering of sequence reads.

Classify metagenomic reads using Kraken2.

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

In silico Legionella pneumophila Sequence Based Typing.

Predict *Listeria monocytogenes* serogroup.

In silico serotype prediction for Listeria monocytogenes.

Calculate genomic distances using MinHash sketches.

Calculate Mash distances between sequences and a reference.

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

Scripts for finding and processing promoter variants upstream of mcr-1.

Serotyping and finetyping of *Neisseria meningitidis*.

Predict serotypes of Neisseria meningitidis from genome assemblies.

MinER assisted species-specific bactopia tool seLectIoN.

Identify species to trigger genus-specific downstream analyses (Merlin).

Identify species from assembly and read data using Mash distances.

Species-level profiling from metagenomic data.

Estimate bacterial species abundance from metagenomic reads.

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

Determine multilocus sequence types (MLST) from bacterial assemblies.

Reconstruct and type plasmids from bacterial genome assemblies.

Reconstruct and type plasmids from a bacterial genome assembly.

Predict antibiotic resistance from sequence reads.

Predict Antimicrobial Resistance (AMR) for supported bacterial species.

Download bacterial genomes from NCBI's RefSeq database.

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

Perform multi-antigen sequence typing of Neisseria gonorrhoeae from genome assemblies.

Remove human reads from sequencing data using nohuman.

Remove human reads from sequencing data.

Predict O-antigen serogroup of Pseudomonas aeruginosa isolates.

Predict serogroups of Pseudomonas aeruginosa from assemblies.

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

Predict penicillin binding protein (PBP) types of Streptococcus pneumoniae from genome assemblies.

Predict prophage regions integrated into bacterial genomes.

Prediction of prophages from bacterial genomes.

Identify plasmid replicon types in bacterial sequences and assemblies.

Identify plasmid replicons in bacterial genome assemblies.

Capsular typing of Streptococcus pneumoniae from Illumina reads.

Perform capsular typing of Streptococcus pneumoniae from NGS data.

Annotate prokaryotic genomes.

Annotate bacterial genomes with functional information.

Quality Assessment Tool for Genome Assemblies.

Evaluate assembly quality using QUAST.

Predict antimicrobial resistance from protein or nucleotide data.

Predict antibiotic resistance from assemblies.

Identify SCCmec elements in Staphylococcus aureus genomes.

Identify SCCmec elements in Staphylococcus aureus genomes.

Remove contaminant sequences from metagenomic data.

Salmonella serotype prediction from genome sequencing data.

Predict Salmonella serotypes from genome assemblies.

k-mer based pipeline to identify the serotype of Streptococcus pneumoniae.

k-mer based Streptococcus pneumoniae serotyping.

Predict Shigella serotypes and differentiate Shigella/EIEC.

Predict serotypes of Shigella from assemblies.

Shigella serotype from Illumina or Oxford Nanopore reads.

Predict serotypes of Shigella from reads or assemblies.

Shigella and EIEC serotyping from assemblies.

Predict serotypes of Shigella and EIEC from assemblies.

Serovar prediction of Salmonella assemblies.

Salmonella In Silico Typing Resource command-line tool.

Rapid haploid variant calling and core genome alignment.

Call variants against a reference genome using Snippy.

Finding spa types in Staphylococcus aureus.

Predict spa types of Staphylococcus aureus from genome assemblies.

Remove human contamination from sequencing reads for SRA submission.

Initialize human read removal database for SRA Human Scrubber.

Scrub human reads from FASTQ files.

Serotype prediction of Streptococcus suis assemblies.

Predict serotypes of Streptococcus suis from genome assemblies.

Primer based SCCmec typing of S. aureus genomes.

Identify SCCmec elements in Staphylococcus aureus genomes using Staphopia method.

Serotype of Shigatoxin producing E. coli using reads/assemblies.

Identify and serotype Shiga toxin-producing E. coli (STEC) from assemblies.

Profile microbial composition using Sylph.

Profile metagenome samples against a database using Sylph.

Search protein query sequences against nucleotide database.

Translate nucleotide query sequences and search nucleotide database.

Profiling tool for Mycobacterium tuberculosis to detect resistance and strain type.

Detect resistance and lineages of Mycobacterium tuberculosis genomes.