Rcorrector has an accuracy higher than or comparable to existing methods, including the only other method (SEECER) designed for RNA-seq reads, and is more time and memory efficient. With a 5 GB memory footprint for 100 million reads, it can be run on virtually any desktop or server. The software is available free of charge under the GNU General Public License from https://github.com/mourisl/Rcorrector/.
Usage: perl run_rcorrector.pl [OPTIONS]
OPTIONS:
Required
-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
Optional
-k INT: kmer_length (<=32, default: 23)
-od STRING: output_file_directory (default: ./)
-t INT: number of threads to use (default: 1)
-trim : allow trimming (default: false)
-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)
-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.