Multi-genome alignment for quality control and contamination screening of next-generation sequencing data
Open Access
- 1 January 2014
- journal article
- research article
- Published by Frontiers Media SA in Frontiers in Genetics
Abstract
The availability of massive amounts of DNA sequence data, from thousands of genomes even in a single project has had a huge impact on our understanding of biology, but also creates several problems for biologists carrying out those experiments. Bioinformatic analysis of sequence data is perhaps the most obvious challenge but upstream of this even basic quality control of sequence run performance is challenging for many users given the volume of data. Users need to be able to assess run quality efficiently so that only high-quality data are passed through to computationally-, financially- and time-intensive processes. There is a clear need to make human review of sequence data as efficient as possible. The multi-genome alignment tool presented here presents next-generation sequencing run data in visual and tabular formats simplifying assessment of run yield and quality, as well as presenting some sample-based quality metrics and screening for contamination from adapter sequences and species other than the one being sequenced.Keywords
This publication has 8 references indexed in Scilit:
- Predicting the molecular complexity of sequencing librariesNature Methods, 2013
- Ultrafast and memory-efficient alignment of short DNA sequences to the human genomeGenome Biology, 2009
- Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysisNucleic Acids Research, 2005
- Automated generation of heuristics for biological sequence comparisonBMC Bioinformatics, 2005
- Robust estimators for expression analysisBioinformatics, 2002
- Base-Calling of Automated Sequencer Traces UsingPhred. I. Accuracy AssessmentGenome Research, 1998
- An improved algorithm for matching biological sequencesJournal of Molecular Biology, 1982
- Identification of common molecular subsequencesJournal of Molecular Biology, 1981