Rcorrector protocols

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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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Maintainer


  • person_outline Liliana Florea <>

Publication for Rcorrector

Rcorrector in pipelines

 (3)
2017
PMCID: 5394691
PMID: 28417958
DOI: 10.1038/srep45125

[…] for the hpg was assembled following the oyster river protocol for transcriptome assembly. in brief, 59 million paired end reads from two individuals (1 male and 1 female) were error corrected using rcorrector version 1.0.2. adapters, as well as bases with a phred score <2 were trimmed using skewer 0.2.2, and assembly was carried out using trinity version 2.2.0, binpacker version 1.0, […]

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

[…] 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 […]

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

[…] 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, […]


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Rcorrector in publications

 (7)
PMCID: 5850769
PMID: 29040712
DOI: 10.1093/molbev/msx268

[…] 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” […]

PMCID: 5549316
PMID: 28789702
DOI: 10.1186/s13104-017-2653-2

[…] 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 […]

PMCID: 5481918
PMID: 28645248
DOI: 10.1186/s12864-017-3840-1

[…] the permutations of this assembly process are described extensively elsewhere [, ]. the testes transcriptome we selected was constructed as described below. the raw reads were error corrected using rcorrector version 1.0.1 [], then subjected to quality trimming (using a threshold of phred <2, as per []) and adapter removal using skewer version 0.1.127 []. these reads were then assembled […]

PMCID: 5850815
PMID: 28453634
DOI: 10.1093/molbev/msx144

[…] 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 […]

PMCID: 5394691
PMID: 28417958
DOI: 10.1038/srep45125

[…] for the hpg was assembled following the oyster river protocol for transcriptome assembly. in brief, 59 million paired end reads from two individuals (1 male and 1 female) were error corrected using rcorrector version 1.0.2. adapters, as well as bases with a phred score <2 were trimmed using skewer 0.2.2, and assembly was carried out using trinity version 2.2.0, binpacker version 1.0, […]


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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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