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Rcorrector specifications

Information


Unique identifier OMICS_26076
Name Rcorrector
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, C++, Perl
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Versioning


No version available

Maintainer


  • person_outline Liliana Florea

Publication for Rcorrector

Rcorrector citations

 (5)
library_books

Signal, Uncertainty, and Conflict in Phylogenomic Data for a Diverse Lineage of Microbial Eukaryotes (Diatoms, Bacillariophyta)

2017
Mol Biol Evol
PMCID: 5850769
PMID: 29040712
DOI: 10.1093/molbev/msx268

[…] enated into single data sets.RNA-seq reads were processed and assembled following recommendations outlined in the Oyster River Protocol (). Briefly, predicted errors in raw reads were corrected using Rcorrector with options “-k 31 -t 15” (). Corrected reads were then trimmed using Trimmomatic (ver. 0.32) with options “ILLUMINACLIP: 2: 40: 15 LEADING: 2 TRAILING: 2 SLIDINGWINDOW: 4: 2 MINLEN: 20” ( […]

call_split

Development of novel genic microsatellite markers from transcriptome sequencing in sugar maple (Acer saccharum Marsh.)

2017
BMC Res Notes
PMCID: 5549316
PMID: 28789702
DOI: 10.1186/s13104-017-2653-2
call_split See protocol

[…] provided in Additional file .Trimmomatic version 0.35 was used to trim raw sequencing reads of adapter sequences and low quality bases []. Kmer-based error correction of RNASeq reads was performed in Rcorrector (kmer length of 31) []. Trimmed and corrected reads were assembled with the Trinity pipeline version r20131110 []. Isoforms from the Trinity pipeline were collapsed and further assembled wi […]

library_books

Recent Sex Chromosome Divergence despite Ancient Dioecy in the Willow Salix viminalis

2017
Mol Biol Evol
PMCID: 5850815
PMID: 28453634
DOI: 10.1093/molbev/msx144

[…] cing errors in trimmed DNA sequencing reads were subsequently corrected using lighter version 1.1.0 () with a k-mer size of 31. Similarly sequencing error in RNA sequencing reads were corrected using Rcorrector () with a k-mer size of 31. Left over contaminating reads from the PhiX spike-in used as internal control in the sequencing process were removed by screening all sequencing reads against th […]

library_books

Co expression of xenopsin and rhabdomeric opsin in photoreceptors bearing microvilli and cilia

2017
eLife
PMCID: 5648526
PMID: 28876222
DOI: 10.7554/eLife.23435.121

[…] n RNA-seq data from several developmental stages from the annelid Owenia fusiformis, transcriptome assemblies were generated using Trimmomatic (RRID:SCR_011848) 0.36 for adapter and quality trimming, Rcorrector () for read error correction and trinity-2.2.1 for read assembly. Blast databases were generated with the NCBI blast+-suite and screened with tblastn (RRID:SCR_011822) for opsins with a que […]

library_books

Characterization of a male reproductive transcriptome for Peromyscus eremicus (Cactus mouse)

2016
PeerJ
PMCID: 5088585
PMID: 27812417
DOI: 10.7717/peerj.2617

[…] th reads from the testes, epididymis and vas deferens using the previously developed Oyster River Protocol for de novo transcriptome assembly pipeline (). Briefly, the reads were error corrected with Rcorrector v1.0.1 (). We used the de novo transcriptome assembler Trinity v2.1.1 (; ). Within the Trinity platform, we ran Trimmomatic () to remove the adapters, and we also trimmed at PHRED < 2, as r […]

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Rcorrector institution(s)
Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
Rcorrector funding source(s)
Supported in part by NSF awards ABI-1159078 and ABI-1356078.

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