Pseudomonas aeruginosa Raw sequence reads

Mapping consists in the alignment of reads (i.e., DNA fragments) obtained through high-throughput genome sequencing to a previously assembled reference sequence. It is a common practice in genomic studies to use a single reference for mapping, usually the "reference genome" of a species - a high-quality assembly. However, the selection of an optimal reference is hindered by intrinsic intra-species genetic variability, particularly in bacteria. Biases/errors due to reference choice for mapping in bacteria have been identified. These are mainly originated in alignment errors due to genetic differences between the reference genome and the read sequences. Eventually, they could lead to misidentification of variants and biased reconstruction of phylogenetic trees (which reflect ancestry between different bacterial lineages). However, a systematic work on the effects of reference choice in different bacterial species is still missing, particularly regarding its impact on phylogenies. This work intended to fill that gap. Impact of reference choice proved to be pervasive in the five bacterial species that we have studied and, in some cases, alterations in phylogenetic trees could lead to incorrect epidemiological inferences. Hence, the use of different reference genomes may be prescriptive to assess the potential biases of mapping.