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Comparative Analysis of Long-Read Transcriptome Assembly Pipelines
- Dubocanin, Danilo
- Advisor(s): Vollmers, Chris
Abstract
Long-read sequencing can overcome some of the barriers in transcriptome assembly
that plague short-read based technologies. Due to their short length, short-reads fail to
span entire transcripts, and this leads to difficulties in discerning proper splice
junctions. Conversely, long-read sequencing can span entire transcripts end-to-end,
and thus can circumvent issues in inferring splice junctions. Multiple long-read
transcriptome assembly pipelines have been developed in recent years but there is no
comprehensive analysis comparing the various pipelines. Some of these pipelines
implement novel approaches to generating transcriptomes using long-reads, while
other pipelines adapted methods originally developed for short-read based
transcriptome assembly. We show that there are significant differences in
transcriptomes assembled on the same data, using different assembly pipelines. Our
analysis further shows that high-level summary statistics can be misleading about
transcriptome quality, as well as the importance of using internalized controls to
validate transcriptome assemblies.
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