One is not enough: on the effects of reference genome for the mapping and subsequent analyses of short-reads
Carlos Valiente-Mullor, Beatriz Beamud, Iván Ansari, Carlos Francés‐Cuesta, Neris García‐González, Lorena Mejía, Paula Ruiz-Hueso, Fernando Gónzález‐Candelas
This paper evaluates how choosing different reference genomes affects short-read mapping and subsequent analyses in five bacterial species, finding significant biases in SNP calling, recombination rates, and phylogenetic trees.
PLoS Computational Biology · Jan 27, 2021Peer-reviewedGenomics