P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
Published 2018 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
Authors
Keywords
RNA-sequencing, Genome scaffolding, Single-molecule sequencing, circRNA
Journal
BMC GENOMICS
Volume 19, Issue 1, Pages -
Publisher
Springer Nature
Online
2018-03-02
DOI
10.1186/s12864-018-4567-3
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- PEP_scaffolder: using (homologous) proteins to scaffold genomes
- (2016) Bai-Han Zhu et al. BIOINFORMATICS
- Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes
- (2016) T.S. Keshava Prasad et al. GENOME RESEARCH
- The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts
- (2016) Zhanjiang Liu et al. Nature Communications
- Rascaf: Improving Genome Assembly with RNA Sequencing Data
- (2016) Li Song et al. Plant Genome
- Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding
- (2016) Shubha Vij et al. PLoS Genetics
- AGOUTI: improving genome assembly and annotation using transcriptome data
- (2016) Simo V. Zhang et al. GigaScience
- Large-scale diversification without genetic isolation in nematode symbionts of figs
- (2016) V. Susoy et al. Science Advances
- Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum
- (2015) Robert VanBuren et al. NATURE
- Assembling large genomes with single-molecule sequencing and locality-sensitive hashing
- (2015) Konstantin Berlin et al. NATURE BIOTECHNOLOGY
- HISAT: a fast spliced aligner with low memory requirements
- (2015) Daehwan Kim et al. NATURE METHODS
- Evolutionary analysis of the female-specific avian W chromosome
- (2015) Linnéa Smeds et al. Nature Communications
- Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling
- (2014) Wei Zhao et al. BMC GENOMICS
- Resolving the complexity of the human genome using single-molecule sequencing
- (2014) Mark J. P. Chaisson et al. NATURE
- Sequencing depth and coverage: key considerations in genomic analyses
- (2014) David Sims et al. NATURE REVIEWS GENETICS
- Ensembl 2015
- (2014) Fiona Cunningham et al. NUCLEIC ACIDS RESEARCH
- circBase: a database for circular RNAs
- (2014) Petar Glažar et al. RNA
- L_RNA_scaffolder: scaffolding genomes with transcripts
- (2013) Wei Xue et al. BMC GENOMICS
- Long Noncoding RNAs: Cellular Address Codes in Development and Disease
- (2013) Pedro J. Batista et al. CELL
- Scaffolding low quality genomes using orthologous protein sequences
- (2012) Y. I. Li et al. BIOINFORMATICS
- Paired-end sequencing of Fosmid libraries by Illumina
- (2012) L. J. S. Williams et al. GENOME RESEARCH
- Landscape of transcription in human cells
- (2012) Sarah Djebali et al. NATURE
- Generation of Long Insert Pairs Using a Cre-LoxP Inverse PCR Approach
- (2012) Ze Peng et al. PLoS One
- SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
- (2012) Ruibang Luo et al. GigaScience
- Fast scaffolding with small independent mixed integer programs
- (2011) L. Salmela et al. BIOINFORMATICS
- GAGE: A critical evaluation of genome assemblies and assembly algorithms
- (2011) S. L. Salzberg et al. GENOME RESEARCH
- Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences
- (2011) Song Gao et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- RNA sequencing reveals two major classes of gene expression levels in metazoan cells
- (2011) D. Hebenstreit et al. Molecular Systems Biology
- Scaffolding pre-assembled contigs using SSPACE
- (2010) Marten Boetzer et al. BIOINFORMATICS
- Fast and accurate long-read alignment with Burrows–Wheeler transform
- (2010) Heng Li et al. BIOINFORMATICS
- SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data
- (2010) Murray P Cox et al. BMC BIOINFORMATICS
- SOPRA: Scaffolding algorithm for paired reads via statistical optimization
- (2010) Adel Dayarian et al. BMC BIOINFORMATICS
- Scaffolding a Caenorhabditis nematode genome with RNA-seq
- (2010) A. Mortazavi et al. GENOME RESEARCH
- Fast and accurate short read alignment with Burrows-Wheeler transform
- (2009) H. Li et al. BIOINFORMATICS
- A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence
- (2008) Osamu Gotoh NUCLEIC ACIDS RESEARCH
Find the ideal target journal for your manuscript
Explore over 38,000 international journals covering a vast array of academic fields.
SearchBecome a Peeref-certified reviewer
The Peeref Institute provides free reviewer training that teaches the core competencies of the academic peer review process.
Get Started