Common workflow language (CWL)-based software pipeline for de novo genome assembly from long- and short-read data.

Pasi K Korhonen,Robin B Gasser,Ross S Hall,Neil D Young

doi:10.1093/gigascience/giz014

Pasi K Korhonen, Robin B Gasser + Show 2 more

Open Access

https://doi.org/10.1093/gigascience/giz014

Copy DOI

Journal: GigaScience	Publication Date: Mar 1, 2019
Citations: 16	License type: CC BY 4.0

Affiliation: University of Melbourne

Abstract

ABSTRACTBackgroundHere, we created an automated pipeline for the de novoassembly of genomes from Pacific Biosciences long-read and Illumina short-read data using common workflow language (CWL). To evaluate the performance of this pipeline, we assembled the nuclear genomes of the eukaryotes Caenorhabditis elegans (∼100 Mb), Drosophila melanogaster (∼138 Mb), and Plasmodium falciparum (∼23 Mb) directly from publicly accessible nucleotide sequence datasets and assessed the quality of the assemblies against curated reference genomes.FindingsWe showed a dependency of the accuracy of assembly on sequencing technology and GC content and repeatedly achieved assemblies that meet the high standards set by the National Human Genome Research Institute, being applicable to gene prediction and subsequent genomic analyses.ConclusionsThis CWL pipeline overcomes current challenges of achieving repeatability and reproducibility of assembly results and offers a platform for the re-use of the workflow and the integration of diverse datasets. This workflow is publicly available via GitHub (https://github.com/vetscience/Assemblosis) and is currently applicable to the assembly of haploid and diploid genomes of eukaryotes.

Highlights

We created an automated pipeline for the de novo assembly of genomes from Pacific Biosciences long-read and Illumina short-read data using common workflow language (CWL)
We showed a dependency of the accuracy of assembly on sequencing technology and GC content and repeatedly achieved assemblies that meet the high standards set by the National Human Genome Research Institute, being applicable to gene prediction and subsequent genomic analyses
Pacific Biosciences (PacBio) reads from HDF5 formatted files that were converted to FASTA formatted files using the program Dextractor

Summary

Introduction

We created an automated pipeline for the de novo assembly of genomes from Pacific Biosciences long-read and Illumina short-read data using common workflow language (CWL). To evaluate the performance of this pipeline, we assembled the nuclear genomes of the eukaryotes Caenorhabditis elegans (∼100 Mb), Drosophila melanogaster (∼138 Mb), and Plasmodium falciparum (∼23 Mb) directly from publicly accessible nucleotide sequence datasets and assessed the quality of the assemblies against curated reference genomes. Conclusions: This CWL pipeline overcomes current challenges of achieving repeatability and reproducibility of assembly results and offers a platform for the re-use of the workflow and the integration of diverse datasets. This workflow is publicly available via GitHub (https://github.com/vetscience/Assemblosis) and is currently applicable to the assembly of haploid and diploid genomes of eukaryotes.

Methods

Results

Discussion

Conclusion