Phylogenetic Heatmaps Highlight Composition Biases in Sequenced Reads
AbstractDue to advancements in sequencing technology, sequence data production is no longer a constraint in the field of microbiology and has made it possible to study uncultured microbes or whole environments using metagenomics. However, these new technologies introduce different biases in metagenomic sequencing, affecting the nucleotide distribution of resulting sequence reads. Here, we illustrate such biases using two methods. One is based on phylogenetic heatmaps (PGHMs), a novel approach for compact visualization of sequence composition differences between two groups of sequences containing the same phylogenetic groups. This method is well suited for finding noise and biases when comparing metagenomics samples. We apply PGHMs to detect noise and bias in the data produced with different DNA extraction protocols, different sequencing platforms and different experimental frameworks. In parallel, we use principal component analysis displaying different clustering of sequences from each sample to support our findings and illustrate the utility of PGHMs. We considered contributions of the read length and GC-content variation and observed that in most cases biases were generally due to the GC-content of the reads. View Full-Text
- Supplementary File 1:
Supplementary (PDF, 691 KB)
Scifeed alert for new publicationsNever miss any articles matching your research from any publisher
- Get alerts for new papers matching your research
- Find out the new papers from selected authors
- Updated daily for 49'000+ journals and 6000+ publishers
- Define your Scifeed now
Choudhari, S.; Grigoriev, A. Phylogenetic Heatmaps Highlight Composition Biases in Sequenced Reads. Microorganisms 2017, 5, 4.
Choudhari S, Grigoriev A. Phylogenetic Heatmaps Highlight Composition Biases in Sequenced Reads. Microorganisms. 2017; 5(1):4.Chicago/Turabian Style
Choudhari, Sulbha; Grigoriev, Andrey. 2017. "Phylogenetic Heatmaps Highlight Composition Biases in Sequenced Reads." Microorganisms 5, no. 1: 4.
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.