37 docs tagged with "run-scope"

Summarize Abricate screening results.

Download and prepare reference databases for ARIBA analysis.

Download pre-compiled datasets required by Bactopia.

Download the Bakta annotation database.

Inference of recombination in bacterial genomes.

Detect and mask recombination events in bacterial phylogenies.

Concatenate multiple CSV or TSV files into a single table.

Join two CSV or TSV files based on common fields.

Download and package the DefenseFinder and CasFinder model databases.

Compute whole-genome Average Nucleotide Identity (ANI).

Calculate Average Nucleotide Identity (ANI) between genomes.

Detect recombination and construct a recombination-free phylogeny.

Detect and filter recombination regions in bacterial alignments.

Efficient phylogenomic inference using Maximum Likelihood.

Construct maximum likelihood phylogenetic trees from alignments.

Rapid alignment-free phylogenomic tree construction.

Create phylogenetic trees using Mash distances.

Download the MIDAS reference database.

Download assemblies and annotation files from NCBI's Assembly database.

Download the nohuman database for human read removal.

Build a pangenome from GFF3 annotations using Panaroo.

Fast and scalable bacterial pangenome analysis using a graph-based approach.

Perform pangenome analysis with optional core-genome phylogeny.

Pangenome Identification and Reconciliation Analysis Tool for Epidemiology (PIRATE).

Build a pangenome from GFF3 annotations using PIRATE.

Create heatmaps of resistance gene presence/absence.

Rapid large-scale prokaryote pan genome analysis.

Build a pangenome from GFF3 annotations using Roary.

Pan-genome wide association studies.

Pan-genome wide association studies.

Core-SNP alignment from Snippy outputs.

Generate core-genome SNP alignment from per-sample Snippy outputs.

Create a SNP distance matrix from a multiple sequence alignment.

Calculate pairwise SNP distances from sequence alignments.

Determine the agr, spa and SCCmec types for _Staphylococcus aureus_ genomes.

Collate TB-Profiler results from multiple samples.

Perform taxonomic classification and estimate bacterial genome sizes.