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

ABSTRACT:

Background

Here, 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.

Findings

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

SUBMITTER: Korhonen PK 

PROVIDER: S-EPMC6451199 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature