A software tool 'CroCo' detects pervasive cross-species contamination in next generation sequencing data.

ABSTRACT:

Background

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.

Results

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 efficie

SUBMITTER: Simion P 

PROVIDER: S-EPMC5838952 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature