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Described in:

Song, L., Florea, L., Rcorrector: Efficient and accurate error correction for Illumina RNA-seq reads. GigaScience. 2015, 4:48.

Copyright (C) 2012-2013, and GNU GPL, by Li Song and Liliana Florea

Rcorrrector includes the program Jellyfish2

What is Rcorrector?

Rcorrector(RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.

Rcorrector can also be applied to other type of sequencing data where the read coverage is non-uniform, such as single-cell sequencing.


  1. Clone the GitHub repo, e.g. with git clone
  2. Run make in the repo directory During the make procedure, the script will check whether you have jellyfish2 in $PATH. If not, it will download and compile jellyfish2 from its repository.


Usage: perl [OPTIONS]
	-s seq_files: comma separated files for single-end data sets
	-1 seq_files_left: comma separated files for the first mate in the paried-end data sets
	-2 seq_files_right: comma separated files for the second mate in the paired-end data sets
	-i seq_files_interleaved: comma sperated files for interleaved paired-end data sets
	-k INT: kmer_length (<=32, default: 23)
	-od STRING: output_file_directory (default: ./)
	-t INT: number of threads to use (default: 1)
	-maxcorK INT: the maximum number of correction within k-bp window (default: 4)
	-wk FLOAT: the proportion of kmers that are used to estimate weak kmer count threshold, lower for more divergent genome (default: 0.95)
	-ek INT: expected number of kmers; does not affect the correctness of program but affects the memory usage (default: 100000000)
	-stdout: output the corrected reads to stdout (default: not used)
	-tmpd temp_file_directory: directory for tempoary files (default: ./)
	-verbose: output some correction information to stdout (default: not used)
	-stage INT: start from which stage (default: 0)
		0-start from begining(storing kmers in bloom filter) ;
		1-start from count kmers showed up in bloom filter;
		2-start from dumping kmer counts into a jf_dump file;
		3-start from error correction.


For each input file, Rcorrector will generate the corresponding output file with "*.cor.fq/fa" in the directory specified by "-od".

In the header line for each read, Rcorrector will append some information.

"cor": some bases of the sequence are corrected
"unfixable_error": the errors could not be corrected
"l:INT m:INT h:INT": the lowest, median and highest kmer count of the kmers from the read


We put a small sample data set, you can run them by:

perl -1 Sample/sample_read1.fq -2 Sample/sample_read2.fq


Terms of use

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received (LICENSE.txt) a copy of the GNU General Public License along with this program; if not, you can obtain one from or by writing to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA


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