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dc.contributor.author MacManes, Matthew D.
dc.contributor.author Eisen, Michael B.
dc.date.accessioned 2013-07-23T17:13:42Z
dc.date.available 2013-07-23T17:13:42Z
dc.date.issued 2013-07-23
dc.identifier doi:10.5061/dryad.km540
dc.identifier.citation MacManes MD, Eisen MB (2013) Improving transcriptome assembly through error correction of high-throughput sequence reads. PeerJ 1: e113.
dc.identifier.uri http://hdl.handle.net/10255/dryad.51509
dc.description The study of functional genomics, particularly in non-model organisms, has been dramatically improved over the last few years by the use of transcriptomes and RNAseq. While these studies are potentially extremely powerful, a computationally intensive procedure, the de novo construction of a reference transcriptome must be completed as a prerequisite to further analyses. The accurate reference is critically important as all downstream steps, including estimating transcript abundance are critically dependent on the construction of an accurate reference. Though a substantial amount of research has been done on assembly, only recently have the pre-assembly procedures been studied in detail. Specifically, several stand-alone error correction modules have been reported on and, while they have shown to be effective in reducing errors at the level of sequencing reads, how error correction impacts assembly accuracy is largely unknown. Here, we show via use of a simulated and empiric dataset, that applying error correction to sequencing reads has significant positive effects on assembly accuracy, and should be applied to all datasets. A complete collection of commands which will allow for the production of Reptile corrected reads is available at https://github.com/macmanes/error_correction/tree/master/scripts
dc.relation.haspart doi:10.5061/dryad.km540/1
dc.relation.haspart doi:10.5061/dryad.km540/2
dc.relation.isreferencedby doi:10.7717/peerj.113
dc.relation.isreferencedby PMID:23904992
dc.title Data from: Improving transcriptome assembly through error correction of high-throughput sequence reads
dc.type Article *
prism.publicationName PeerJ

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Title Simulated Illumina Reads
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Description 30 million 100nt PE reads. These are the _2 reads.
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Title Simulated Illumina Reads
Downloaded 30 times
Description 30 million PE 100nt simulated Illumina reads. These are the _1 files.
Download sim.reads.left.fq.gz (1.743 Gb)
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