Described in:

Song, L., Florea, L. and Langmead, B., Lighter: Fast and Memory-efficient Sequencing Error Correction without Counting. Genome Biol. 2014 Nov 15;15(11):509.

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

Lighter includes source code from the bloom C++ Bloom filter library. bloom is distributed under the Mozilla Public License (MPL) v1.1.

Lighter is a kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.

1. Clone the GitHub repo, e.g. with git clone https://github.com/mourisl/Lighter.git
2. Run make in the repo directory

Lighter is small and portable, with pthreads and zlib being the only library dependency.

Usage: ./lighter [OPTIONS]
OPTIONS:
Required parameters:
    -r seq_file: seq_file is the path to the sequence file. Can use multiple -r to specifiy multiple sequence files
                     The file can be fasta and fastq, and can be gzip'ed with extension *.gz. 
                     When the input file is *.gz, the corresponding output file will also be gzip'ed.
    -k kmer_length genome_size alpha
    		or
    -K kmer_length genome_size
Other parameters:
    -od output_file_directory: (default: ./)
    -t num_of_threads: number of threads to use (default: 1)
    -maxcor: the maximum number of correction for within a kmer_length window (default: 4)
    -trim: allow trimming (default: false)
    -discard: discard unfixable reads. Will LOSE paired-end matching when discarding (default: false)
    -noQual: ignore the quality socre (default: false)
    -newQual ascii_quality_score: set the quality for the bases corrected to the specified score (default: not used)
    -zlib compress_level: set the compression level(1-9) of gzip (default: 1)
    -h: print the help message and quit
    -v: print the version information and quit

NOTICE: genome_size does not need to be accurate, but it should be at least as large as the size of the sequenced genome.
        alpha is the sampling rate and decided by the user. A rule of thumb: alpha=(7/C), where C is the average coverage of the data set.
    When using "-K" instead of "-k", Lighter will go through the reads an extra pass to decide C. And for "-K", genome_size should be relative accurate.

For each input file (specified by -r), Lighter will create a corresponding file containing the corrected reads in the directory specified by "-od". If the name of a read file is like A.fq or A.fastq, the corresponding output file name is A.cor.fq. For A.fa or A.fasta, the output file is A.cor.fa. For A.fastq.gz or A.fq.gz, the output file is A.cor.fq.gz. For A.fasta.gz or A.fa.gz, the output file is A.cor.fa.gz.

For each header line, Lighter will append some information regarding the correction result.

"cor": some bases of the sequence are corrected
"bad_suffix", "bad_prefix": the errors in the suffix or prefix of indicated length could not be corrected
"unfixable_error": the errors could not be corrected
There are some two-characters string to indicate the reason why Lighter could not correct the errors:
	"lc": low coverage
	"ak": ambiguous candidate kmer
	"oc": over corrected

Suppose the data set is from E.Coli whose genome size is about 4.7M. If the data set has 3.3M reads in total with read length 100bp, then the average coverage is about 70x and we can set the alpha to be 7/70=0.1.

Single-end data set:

./lighter -r read.fq -k 17 5000000 0.1 -t 10

Paired-end data set:

./lighter -r left.fq -r right.fq -k 17 5000000 0.1 -t 10

Instead of "-k 17 5000000 0.1", you can use "-K 17 4700000" so that Lighter will go through the data set an extra pass to decide alpha.

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 http://www.gnu.org/licenses/gpl.txt or by writing to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA

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