BactPrep: A user-friendly whole-genome sequencing analysis platform for the detection of homologous recombination and horizontal gene transfer in bacteria - Sample Dataset

This is the dataset used as the sample dataset for the pipeline BactPrep. This dataset consists of 218 <em>Streptococcus pneumoniae</em> PMEN1 WGS assemblies collected from the year 1984 - 2008 from 22 unique countries globally. The raw sequencing data was originally published in the work: Rapid pneumococcal evolution in response to clinical interventions (doi: 10.1371/journal.ppat.1002745) under the bioproject PRJEB2085. We have assembled the raw sequences records with the following steps: 1) raw reads were first quality checked using fastQC 0.11.9; 2) adapters and low quality reads were removed using Trimmomatic 0.39 with parameter “ILLUMINACLIP:TruSeq2-PE.fa:2:30:10:2:keepBothReads LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36”; 3) trimmed reads were error-corrected and assembled into WGS assemblies using SPAdes 3.15.0 with parameters "--careful --mismatch-correction”.