NAME

       lighter - fast and memory-efficient sequencing error corrector

SYNOPSIS

       lighter [OPTIONS]

DESCRIPTION

       Lighter  is a fast, memory-efficient tool for correcting sequencing errors. Lighter avoids
       counting k-mers. Instead, it uses a pair of Bloom filters, one holding  a  sample  of  the
       input  k-mers  and  the other holding k-mers likely to be correct. As long as the sampling
       fraction is adjusted in inverse proportion to the depth of sequencing, Bloom  filter  size
       can  be  held constant while maintaining near-constant accuracy.  Lighter is parallelized,
       uses no secondary storage, and is both faster and  more  memory-efficient  than  competing
       approaches while achieving comparable accuracy.

OPTIONS:

   Required parameters:
       -r  seq_file:  seq_file  is  the path to the sequence file. Can use multiple -r to specify
       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: (see README for information on setting alpha)
              or

       -K kmer_length genom_size: in this case, the genome size should be relative accurate.

   Other parameters:
       -od output_file_directory: (default: ./)

       -t num_of_threads: number of threads to use (default: 1)

       -maxcor INT: the maximum number of corrections within a 20bp 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)

       -saveTrustedKmers  file:  save the trusted kmers to specified file then stop (default: not
              used)

       -loadTrustedKmers file: directly get solid kmers from specified file (default: not used)

       -zlib compress_level: set the compression level(0-9) of gzip (default: 1)

       -h: print the help message and quit

       -v: print the version information and quit

AUTHOR

        This manpage was written by Andreas Tille for the Debian distribution and
        can be used for any other usage of the program.