Hybrid Enterobacteriaceae assemblies using PacBio+Illumina or ONT+Illumina sequencing

Data associated with: De Maio, Shaw, et al. on behalf of the REHAB consortium (2019), Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes. biorxiv 530824 Illumina sequencing allows rapid, cheap and accurate whole genome bacterial analyses, but short reads (<300 bp) do not usually enable complete genome assembly. Long read sequencing greatly assists with resolving complex bacterial genomes, particularly when combined with short-read Illumina data (hybrid assembly). However, it is not clear how different long-read sequencing methods impact on assembly accuracy. In this study, we compared hybrid assemblies for 20 bacterial isolates, including two reference strains, using Illumina sequencing and long reads from either Oxford Nanopore Technologies (ONT) or from SMRT Pacific Biosciences (PacBio) sequencing platforms. This set of files includes all hybrid assemblies produced using Unicycler with different sequencing approaches and strategies. Each isolate has 8 assemblies = 4 x ONT-Illumina + 4 x PacBio-Illumina. There are a total of 158 assemblies as two assemblies did not finish (8x20 - 2 = 160 - 2 = 158). Assemblies were produced from different long read preparation strategies:• Basic: no filtering or correction of reads (i.e. all long reads available used for assembly). • Corrected: Long reads were error-corrected and subsampled (preferentially selecting longest reads) to 30-40x coverage using Canu (v1.5, https://github.com/marbl/canu) with default options. • Filtered: long reads were filtered using Filtlong (v0.1.1, https://github.com/rrwick/Filtlong) by using Illumina reads as an external reference for read quality and either removing 10% of the worst reads or by retaining 500Mbp in total, whichever resulted in fewer reads. We also removed reads shorter than 1kb and used the --trim and --split 250 options. • Subsampled: we randomly subsampled long reads to leave approximately 600Mbp (corresponding to a long read coverage around 100x). Assembly file names have the following format: ${sample-name}_${preparation-strategy}_${long-read-sequencing}.fastae.g. for sample CFT073 the filtered PacBio-Illumina assembly is: CFT073_filtered_pacbio.fasta See the associated preprint for more details: https://doi.org/10.1101/530824