ArticleBMC genomics2013
L_RNA_scaffolder: scaffolding genomes with transcripts.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 82 papers.
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Who cites it
82 citing papers in PubMed.
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- Establishing genome sequencing and assembly for non-model and emerging model organisms: a brief guide.Frontiers in zoology · 2025Review
- Genome sequence of the Mediterranean red coral Corallium rubrum.BMC research notes · 2024Article
- First draft reference genome and annotation of the alternative oil species Physaria fendleri.G3 (Bethesda, Md.) · 2024Article
- Ecological genomics in the Northern krill uncovers loci for local adaptation across ocean basins.Nature communications · 2024Article
- Whole-genome duplication in an algal symbiont bolsters coral heat tolerance.Science advances · 2024Article
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- Mutational profile of the regenerative process and de novo genome assembly of the planarian Schmidtea polychroa.Nucleic acids research · 2024Article
- Integrated Genome Sequencing and Transcriptome Analysis Identifies Candidate Pathogenicity Genes fromJournal of fungi (Basel, Switzerland) · 2024Article
- Massive genome reduction predates the divergence of Symbiodiniaceae dinoflagellates.The ISME journal · 2024Article
- Multi-omics analysis reveals the molecular response to heat stress in a "red tide" dinoflagellate.Genome biology · 2023Article
- The genome of the reef-building glass spongeRoyal Society open science · 2023Article
- Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2.Nature communications · 2023Article
- A draft Diabrotica virgifera virgifera genome: insights into control and host plant adaption by a major maize pest insect.BMC genomics · 2023Article
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- Genomic signatures of recent convergent transitions to social life in spiders.Nature communications · 2022Article
- Transcript- and annotation-guided genome assembly of the European starling.Molecular ecology resources · 2022Article
- Molecular insights into high-altitude adaption and acclimatisation ofLife science alliance · 2022Article
- Article
22 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGeneration of large mate-pair libraries is necessary for de novo genome assembly but the procedure is complex and time-consuming. Furthermore, in some complex genomes, it is hard to increase the N50 length even with large mate-pair libraries, which leads to low transcript coverage. Thus, it is necessary to develop other simple scaffolding approaches, to at least solve the elongation of transcribed fragments.
resultsWe describe L_RNA_scaffolder, a novel genome scaffolding method that uses long transcriptome reads to order, orient and combine genomic fragments into larger sequences. To demonstrate the accuracy of the method, the zebrafish genome was scaffolded. With expanded human transcriptome data, the N50 of human genome was doubled and L_RNA_scaffolder out-performed most scaffolding results by existing scaffolders which employ mate-pair libraries. In these two examples, the transcript coverage was almost complete, especially for long transcripts. We applied L_RNA_scaffolder to the highly polymorphic pearl oyster draft genome and the gene model length significantly increased.
conclusionsThe simplicity and high-throughput of RNA-seq data makes this approach suitable for genome scaffolding. L_RNA_scaffolder is available at http://www.fishbrowser.org/software/L_RNA_scaffolder.
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