proBait - Tutorials

This dataset contains the 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. 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.本数据集包含proBait教程中所用的数据文件。proBait是一款用于设计靶向捕获实验所需捕获探针/诱饵（capture probes/baits）的生物信息学开源工具，可在GitHub平台免费获取。本数据集涵盖三个教程，分别对应三类具体应用场景。 Spneumo 本教程旨在演示如何生成一组捕获探针/诱饵，以覆盖某一细菌物种的遗传多样性。本教程中，我们下载了截至2025年11月22日NCBI RefSeq数据库中所有已发布的肺炎链球菌完整基因组，用于筛选具备代表性的基因组集合以开展探针/诱饵设计。利用多位点序列分型（Multi-Locus Sequence Typing, MLST）工具对每条基因组的序列型（Sequence Type, ST）进行鉴定，按不同序列型筛选代表性基因组，最终从初始下载的258条完整基因组中筛选得到119条完整基因组作为分析数据集。将该119条完整基因组作为输入提交给proBait，即可生成包含47937条捕获探针/诱饵的集合。本数据集包含提交给proBait的输入基因组、FASTA格式的捕获探针/诱饵集合，以及proBait生成的覆盖度评估报告。 Multispecies 本教程演示了如何构建一组捕获探针/诱饵，以同时捕获多种细菌物种的靶序列。本案例聚焦于肺炎链球菌与化脓性链球菌。本数据集包含两个物种各两条基因组：一条为该物种的参考基因组，另一条为代表特定谱系的完整基因组，用于模拟需针对特定菌株（如新兴谱系菌株）优化捕获效率的应用场景。将该四条完整基因组作为输入提交给proBait，即可生成包含33690条捕获探针/诱饵的集合。本数据集包含提交给proBait的输入基因组、FASTA格式的捕获探针/诱饵集合，以及proBait生成的覆盖度评估报告。 MEGARes 用于捕获探针/诱饵设计的输入数据不必局限于基因组组装结果，目标DNA序列只要以FASTA格式提供即可为任意类型的靶序列。本教程中，我们利用proBait设计一组捕获探针/诱饵，以捕获一批靶基因集合，具体为MEGARes数据库58个类别各自的代表性序列。将包含各类别代表性序列的FASTA文件作为输入提交给proBait，即可生成包含46561条捕获探针/诱饵的集合。本数据集包含提交给proBait的、包含MEGARes各类别代表性序列的FASTA文件、FASTA格式的捕获探针/诱饵集合，以及proBait生成的覆盖度评估报告。