A software tool ‘CroCo’ detects pervasive cross-species contamination in next generation sequencing data

• DOI: 10.1186/s12915-018-0486-7
• Publication Date: 2018-03-05T11:44:34Z
• Authors: Paul Simion; Khalid Belkhir; Clémentine François; Julien Veyssier; Jochen C. Rink; Michaël Manuel; Hervé Philippe; Maximilian J. Tel...
• Keywords: Multiplex

Multiple RNA samples are frequently processed together and often mixed before multiplex sequencing in the same run. While different can be separated post using sample barcodes, possibility of cross contamination between biological from species that have been or sequenced parallel has potential to extremely deleterious for downstream analyses. We present CroCo, a software package identifying removing such contaminants assembled transcriptomes. Using multiple, recently published sequence datasets, we show is consistently at varying levels real data. simulated data, demonstrate CroCo detects efficiently correctly. example molecular phylogenetic dataset, contaminants, if not eliminated, decisive, impact on comparative Cross pervasive new datasets and, undetected, serious effects database-independent, multi-platform tool, designed ease use, accurately removes transcriptomes avoid these problems. suggest use should become standard cleaning step when processing multiple transcriptome sequencing.