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L_RNA_scaffolder specifications

Information


Unique identifier OMICS_27433
Name L_RNA_scaffolder
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format PSL
Output format FASTA
Biological technology Illumina
Operating system Unix/Linux
Programming languages C++, Perl, Shell (Bash)
Computer skills Advanced
Stability Stable
Maintained No

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Additional information


http://www.fishbrowser.org/software/L_RNA_scaffolder/index.php/Home/Index/documentation.html

Publication for L_RNA_scaffolder

L_RNA_scaffolder citations

 (23)
library_books

Comparative genomics of bdelloid rotifers: Insights from desiccating and nondesiccating species

2018
PLoS Biol
PMCID: 5916493
PMID: 29689044
DOI: 10.1371/journal.pbio.2004830

[…] ffolded with the PacBio library using SSPACE-LongRead v1.1 []. RNASeq reads for A. ricciae were assembled de novo using Trinity v2.2.0 [] (default parameters) and used for additional scaffolding with L_RNA_Scaffolder [] and SCUBAT v2 []. An available transcriptome for R. magnacalcarata [] was similarly utilised. A final round of assembly ‘polishing’ was performed using Redundans v0.12b [], and sca […]

library_books

The genome of Austrofundulus limnaeus offers insights into extreme vertebrate stress tolerance and embryonic development

2018
BMC Genomics
PMCID: 5819677
PMID: 29463212
DOI: 10.1186/s12864-018-4539-7

[…] scaffold two contigs (−k = 3, −a = 0.7) []. The resulting scaffolds were then merged between Allpaths-LG and JR-assembler to provide the best representation of unique scaffolds from both assemblies. L_RNA_Scaffolder software was used to improve the assembly by breaking apart and rejoining poorly supported scaffolds using a preliminary transcriptome derived from a 12 dpd embryo RNA-seq dataset (Ri […]

library_books

Draft genomes of two blister beetles Hycleus cichorii and Hycleus phaleratus

2018
GigaScience
PMCID: 5905561
PMID: 29444297
DOI: 10.1093/gigascience/giy006

[…] following text. First, we used Platanus software (Platanus, RRID:SCR_015531) [] to construct the contigs. We took the paired-end information to scaffolds by SSPACE (RRID:SCR_005056) []. We then used L_RNA_scaffolder [] with ESTs produced by RNA-seq (available from accession numbers PRJNA349771 and PRJNA381455) to construct scaffolds, and we used the information of homolog proteins, which includes […]

library_books

A hybrid hierarchical genome assembly strategy to sequence the invasive golden mussel, Limnoperna fortunei

2017
GigaScience
PMCID: 5836269
PMID: 29267857
DOI: 10.1093/gigascience/gix128

[…] tial drafts [, ]. PacBio long reads allowed us to increase the N50 to 32 Kb and to reduce the number of scaffolds from millions to 61 102, using the DBG2OLC [] assembler. Finally, interactive runs of L_RNA_scaffolder [] using the transcriptomes (Table ) rendered the final result of N50 312 Kb in 20 548 scaffolds. It is important to note that assembly statistics can perform better for genomes assem […]

library_books

Comparative analysis of the genomes of Stylophora pistillata and Acropora digitifera provides evidence for extensive differences between species of corals

2017
Sci Rep
PMCID: 5730576
PMID: 29242500
DOI: 10.1038/s41598-017-17484-x

[…] age) and four mate-pair libraries (96x coverage) were de novo assembled with ALLPATHS-LG release 48961 using parameter HAPLOIDIFY = True, and transcriptome data was used to scaffold the assembly with L_RNA_Scaffolder. All Illumina sequencing libraries were used for scaffolding and gap filling using SSPACE version 1.2 and GapFiller version 1.11 iteratively for 3 rounds. The above-described procedur […]

library_books

Structure and Diversity of the Rhesus Macaque Immunoglobulin Loci through Multiple De Novo Genome Assemblies

2017
Front Immunol
PMCID: 5663730
PMID: 29163486
DOI: 10.3389/fimmu.2017.01407

[…] rying in length between 1,500 and 20,000 bp, and these were used to further scaffold the contigs using SSPACE-LongReadv1.1 (). Finally, we used transcriptome data () and scaffolded the assembly using L_RNA_scaffolder (). 29 scaffolds representing the IGH locus were identified using African green monkey, cynomolgus macaque and human IGH as queries in BLAST+ to obtain the contigs representing the rh […]

Citations

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L_RNA_scaffolder institution(s)
The Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China; Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China; Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
L_RNA_scaffolder funding source(s)
Supported by China Ministry of Science and Technology 863 Hi-Tech Research and Development Program (No. 2011AA100401), and Special Scientific Research Funds for Central Non-profit Institutes, Chinese Academy of Fishery Science (2012C014).

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