ArticleGigaScience2019
Common workflow language (CWL)-based software pipeline for de novo genome assembly from long- and short-read data.
Article in GigaScience, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 18 citations in OpenAlex.
- Enhanced Genomic and Transcriptomic Resources forInternational journal of molecular sciences · 2024Article
- From contigs towards chromosomes: automatic improvement of long read assemblies (ILRA).Briefings in bioinformatics · 2023Article
- The redlegged earth mite draft genome provides new insights into pesticide resistance evolution and demography in its invasive Australian range.Journal of evolutionary biology · 2023Article
- Software pipelines for RNA-Seq, ChIP-Seq and germline variant calling analyses in common workflow language (CWL).Frontiers in bioinformatics · 2023Article
- Chromosome-scale Echinococcus granulosus (genotype G1) genome reveals the Eg95 gene family and conservation of the EG95-vaccine molecule.Communications biology · 2022Article
- ARAMIS: From systematic errors of NGS long reads to accurate assemblies.Briefings in bioinformatics · 2021Article
- High-quality nuclear genome for Sarcoptes scabiei-A critical resource for a neglected parasite.PLoS neglected tropical diseases · 2020Article
- Article
- Quantifying the benefit offered by transcript assembly with Scallop-LR on single-molecule long reads.Genome biology · 2019Article
- Long-read sequencing reveals a 4.4 kb tandem repeat region in the mitogenome of Echinococcus granulosus (sensu stricto) genotype G1.Parasites & vectors · 2019Article
- Common workflow language (CWL)-based software pipeline for de novo genome assembly from long- and short-read data.GigaScience · 2019Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundHere, 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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.