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Parallelization of the Trinity Pipeline for De Novo Transcriptome Assembly

Authors: Vipin Sachdeva; Chang Sik Kim; Kirk E. Jordan; Martyn D. Winn;

Parallelization of the Trinity Pipeline for De Novo Transcriptome Assembly

Abstract

This paper details a distributed-memory implementation of Chrysalis, part of the popular Trinity workflow used for de novo transcripto me assembly. We have implemented changes to Chrysalis, which was previously multi-threaded for shared-memory architectures, to change it to a hybrid implementation which uses both MPI and OpenMP. With the new hybrid implementation, we report speedups of about a factor of twenty for both Graph From Fasta and Reads To Transcripts on an iDataPlex cluster for a sugar beet dataset containing around 130 million reads. Along with the hybrid implementation, we also use PyFasta to speed up Bowtie execution by a factor of three which is also part of the Trinity workflow. Overall, we reduce the runtime of the Chrysalis step of the Trinity workflow from over 50 hours to less than 5 hours for the sugar beet dataset. By enabling the use of multi-node clusters, this implementation is a significant step towards making de novo transcripto me assembly feasible for ever bigger transcripto me datasets.

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
4
Average
Average
Top 10%
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