ArticleBMC biology2018
A software tool 'CroCo' detects pervasive cross-species contamination in next generation sequencing data.
Article in BMC biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed.
- Fragmentation of Long Reads Enables Reliable Mitogenome Assembly From Whole-Genome Amplification Data With Pervasive Palindromic Reads.Molecular ecology resources · 2026Article
- CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomic data.Nature communications · 2026Article
- Origin of subgenomes in the circumboreal, allopolyploid, carnivorous plant Drosera anglica.American journal of botany · 2026Article
- Venom gland transcriptomics and bioactivity profiling suggest bifunctional hyaluronidase activity in the venom ofFrontiers in molecular biosciences · 2026Article
- A Phylogenomic Backbone for Acoelomorpha Inferred From Transcriptomic Data.Systematic biology · 2025Article
- Multiple Displacement Amplification Facilitates SMRT Sequencing of Microscopic Animals and the Genome of the Gastrotrich Lepidodermella squamata (Dujardin 1841).Genome biology and evolution · 2024Article
- Dataset of PLA2 family identified from transcriptomic high-throughput sequencing ofData in brief · 2024Article
- PhyloAln: A Convenient Reference-Based Tool to Align Sequences and High-Throughput Reads for Phylogeny and Evolution in the Omic Era.Molecular biology and evolution · 2024Article
- ContScout: sensitive detection and removal of contamination from annotated genomes.Nature communications · 2024Article
- GTax: improving de novo transcriptome assembly by removing foreign RNA contamination.Genome biology · 2024Article
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- Identifying and addressing methodological incongruence in phylogenomics: A review.Evolutionary applications · 2023Review
- Maturases and Group II Introns in the Mitochondrial Genomes of the Deepest Jakobid Branch.Genome biology and evolution · 2023Article
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- Background Filtering of Clinical Metagenomic Sequencing with a Library Concentration-Normalized Model.Microbiology spectrum · 2022Article
- A Practical Guide to Design and Assess a Phylogenomic Study.Genome biology and evolution · 2022Article
- A modified protocol with less clean-up steps increased efficiency and product yield of sequencing library preparation.3 Biotech · 2022Article
- Phylogenomic resolution of the root of Panpulmonata, a hyperdiverse radiation of gastropods: new insight into the evolution of air breathing.Proceedings. Biological sciences · 2022Article
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Authors and funding
8 authors.
Funding
Abstract
backgroundMultiple 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.
resultsWe 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.
conclusionsCross 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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.