ArticleBMC bioinformatics2014
QTrim: a novel tool for the quality trimming of sequence reads generated using the Roche/454 sequencing platform.
Article in BMC bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Integrated COVID-19 Predictor: Differential expression analysis to reveal potential biomarkers and prediction of coronavirus using RNA-Seq profile data.Computers in biology and medicine · 2022Article
- Noncoding RNAs in apoptosis: identification and function.Turkish journal of biology = Turk biyoloji dergisi · 2022Review
- Genome-resolved metagenomics using environmental and clinical samples.Briefings in bioinformatics · 2021Review
- Genome-Wide Identification of Epigenetic Regulators inInternational journal of molecular sciences · 2020Article
- Gene Expression Profiling Indicated Diverse Functions and Characteristics of Core Genes in Pea Aphid.Insects · 2020Article
- Metabolic Dependencies Underlie Interaction Patterns of Gut Microbiota During Enteropathogenesis.Frontiers in microbiology · 2019Article
- Article
- On the study of microbial transcriptomes using second- and third-generation sequencing technologies.Journal of microbiology (Seoul, Korea) · 2016Review
- The major histocompatibility complex in Old World camelids and low polymorphism of its class II genes.BMC genomics · 2016Article
- Whole Genome Sequencing of the Asian Arowana (Scleropages formosus) Provides Insights into the Evolution of Ray-Finned Fishes.Genome biology and evolution · 2015Article
- Ability to develop broadly neutralizing HIV-1 antibodies is not restricted by the germline Ig gene repertoire.Journal of immunology (Baltimore, Md. : 1950) · 2015Article
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6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundMany high throughput sequencing (HTS) approaches, such as the Roche/454 platform, produce sequences in which the quality of the sequence (as measured by a Phred-like quality scores) decreases linearly across a sequence read. Undertaking quality trimming of this data is essential to enable confidence in the results of subsequent downstream analysis. Here, we have developed a novel, highly sensitive and accurate approach (QTrim) for the quality trimming of sequence reads generated using the Roche/454 sequencing platform (or any platform with long reads that outputs Phred-like quality scores).
resultsThe performance of QTrim was evaluated against all other available quality trimming approaches on both poor and high quality 454 sequence data. In all cases, QTrim appears to perform equally as well as the best other approach (PRINSEQ) with these two methods significantly outperforming all other methods. Further analysis of the trimmed data revealed that the novel trimming approach implemented in QTrim ensures that the prevalence of low quality bases in the resulting trimmed data is substantially lower than PRINSEQ or any of the other approaches tested.
conclusionsQTrim is a novel, highly sensitive and accurate algorithm for the quality trimming of Roche/454 sequence reads. It is implemented both as an executable program that can be integrated with standalone sequence analysis pipelines and as a web-based application to enable individuals with little or no bioinformatics experience to quality trim their sequence data.
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