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Optimizing error correction of RNAseq reads

View ORCID ProfileMatthew D. MacManes
doi: https://doi.org/10.1101/020123
Matthew D. MacManes
1Department of Molecular Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824. USA
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ABSTRACT

Motivation: The correction of sequencing errors contained in Illumina reads derived from genomic DNA is a common pre-processing step in many de novo genome assembly pipelines, and has been shown to improved the quality of resultant assemblies. In contrast, the correction of errors in transcriptome sequence data is much less common, but can potentially yield similar improvements in mapping and assembly quality. This manuscript evaluates several popular read-correction tool’s ability to correct sequence errors commonplace to transcriptome derived Illumina reads.

Results: I evaluated the efficacy of correction of transcriptome derived sequencing reads using using several metrics across a variety of sequencing depths. This evaluation demonstrates a complex relationship between the quality of the correction, depth of sequencing, and hardware availability which results in variable recommendations depending on the goals of the experiment, tolerance for false positives, and depth of coverage. Overall, read error correction is an important step in read quality control, and should become a standard part of analytical pipelines.

Availability: Results are non-deterministically repeatable using AMI:ami-3dae4956 (MacManes_EC_2015) and the Makefile available here: https://goo.gl/oVIuE0

Contact: matthew.macmanes{at}unh.edu and @PeroMHC

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted May 29, 2015.
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Optimizing error correction of RNAseq reads
Matthew D. MacManes
bioRxiv 020123; doi: https://doi.org/10.1101/020123
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Optimizing error correction of RNAseq reads
Matthew D. MacManes
bioRxiv 020123; doi: https://doi.org/10.1101/020123

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