proBait - Tutorials

This dataset contains the compressed data files used in the proBait tutorials. proBait is a bioinformatics tool for designing capture probes/baits used in target capture experiments. proBait is open-source software that is freely available on GitHub. There are three tutorials, each representing a specific use case. Spneumo The objective of this tutorial is to demonstrate how to generate a set of baits/probes to capture the diversity of a bacterial species. In this tutorial, all the complete genomes of Streptococcus pneumoniae available on NCBI RefSeq, as of 22/11/2025, were downloaded to select a representative set of genomes for bait/probe design. The Sequence Type (ST) of each genome was determined with the MLST tool to select a representative genome per distinct ST, ending up with a dataset containing 119 complete genomes (from a total of 258 complete genomes that were initially downloaded). The 119 complete genomes were given as input to proBait to generate a set of 47,937 baits/probes. This dataset includes the genomes given as input to proBait, the set of baits/probes in FASTA format, and the coverage evaluation report created by proBait. For demonstration purposes and to reduce file size, the evaluation report in HTML format only includes the coverage data for 15 genomes. Multispecies This tutorial demonstrates how to create a set of baits/probes to capture multiple bacterial species. In this case, we focused on Streptococcus pneumoniae and Streptococcus pyogenes. The dataset includes two genomes for each of the two species, one reference genome for the species, and a complete genome representative of a specific lineage to simulate a scenario where there is interest in optimizing capturing efficiency for particular strains (e.g. belonging to emerging lineages). The four complete genomes were given as input to proBait to generate a set of 33,690 baits/probes. This dataset includes the genomes given as input to proBait, the set of baits/probes in FASTA format, and the coverage evaluation report created by proBait. MEGARes The inputs for bait/probe set design do not have to be genome assemblies. The target DNA sequences can be anything as long as they are provided in FASTA format. In this tutorial, proBait is used to design a set of baits/probes to capture a collection of target genes, more particularly, the representative sequences for each of the 58 classes of the MEGARes database. The FASTA files containing the representative sequences for each class were given as input to proBait to generate a set of 46,561 baits/probes. This dataset includes the FASTA files containing the representative sequence for the MEGARes classes given as input to proBait, the set of baits/probes in FASTA format, and the coverage evaluation report created by proBait. For demonstration purposes and to reduce file size, the evaluation report in HTML format only includes the coverage data for the representative sequences of 10 MEGARes classes.