↓ Skip to main content

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

Overview of attention for article published in BMC Biology, March 2018
Altmetric Badge

Mentioned by

twitter
72 X users

Citations

dimensions_citation
86 Dimensions

Readers on

mendeley
88 Mendeley
You are seeing a free-to-access but limited selection of the activity Altmetric has collected about this research output. Click here to find out more.
Title
A software tool ‘CroCo’ detects pervasive cross-species contamination in next generation sequencing data
Published in
BMC Biology, March 2018
DOI 10.1186/s12915-018-0486-7
Pubmed ID
Authors

Paul Simion, Khalid Belkhir, Clémentine François, Julien Veyssier, Jochen C. Rink, Michaël Manuel, Hervé Philippe, Maximilian J. Telford

Abstract

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

X Demographics

X Demographics

The data shown below were collected from the profiles of 72 X users who shared this research output. Click here to find out more about how the information was compiled.
Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 88 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 88 100%

Demographic breakdown

Readers by professional status Count As %
Student > Master 17 19%
Researcher 17 19%
Student > Ph. D. Student 17 19%
Student > Bachelor 7 8%
Student > Doctoral Student 5 6%
Other 9 10%
Unknown 16 18%
Readers by discipline Count As %
Agricultural and Biological Sciences 35 40%
Biochemistry, Genetics and Molecular Biology 21 24%
Computer Science 5 6%
Environmental Science 4 5%
Chemical Engineering 1 1%
Other 2 2%
Unknown 20 23%