GenomicsPLoS Computational BiologyPeer-reviewed
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…·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.
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