ArticleBioinformatics (Oxford, England)2013
Scaffolding low quality genomes using orthologous protein sequences.
Article in Bioinformatics (Oxford, England), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Phylogenetic approaches to identifying fragments of the same gene, with application to the wheat genome.Bioinformatics (Oxford, England) · 2019Article
- Article
- Improving draft genome contiguity with reference-derived in silico mate-pair libraries.GigaScience · 2018Article
- P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads.BMC genomics · 2018Article
- PEP_scaffolder: using (homologous) proteins to scaffold genomes.Bioinformatics (Oxford, England) · 2016Article
- A transcriptional blueprint for a spiral-cleaving embryo.BMC genomics · 2016Article
- A scalable and accurate targeted gene assembly tool (SAT-Assembler) for next-generation sequencing data.PLoS computational biology · 2014Article
- Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.GigaScience · 2013Article
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Authors and funding
2 authors.
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Abstract
motivationThe ready availability of next-generation sequencing has led to a situation where it is easy to produce very fragmentary genome assemblies. We present a pipeline, SWiPS (Scaffolding With Protein Sequences), that uses orthologous proteins to improve low quality genome assemblies. The protein sequences are used as guides to scaffold existing contigs, while simultaneously allowing the gene structure to be predicted by homology.
resultsTo perform, SWiPS does not depend on a high N50 or whole proteins being encoded on a single contig. We tested our algorithm on simulated next-generation data from Ciona intestinalis, real next-generation data from Drosophila melanogaster, a complex genome assembly of Homo sapiens and the low coverage Sanger sequence assembly of Callorhinchus milii. The improvements in N50 are of the order of ∼20% for the C.intestinalis and H.sapiens assemblies, which is significant, considering the large size of intergenic regions in these eukaryotes. Using the CEGMA pipeline to assess the gene space represented in the genome assemblies, the number of genes retrieved increased by >110% for C.milii and from 20 to 40% for C.intestinalis. The scaffold error rates are low: 85-90% of scaffolds are fully correct, and >95% of local contig joins are correct. AVAILABILITY: SWiPS is available freely for download at http://www.well.ox.ac.uk/∼yli142/swips.html. CONTACT: yang.li@well.ox.ac.uk or copley@well.ox.ac.uk
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