NAME

       racon - consensus module for raw de novo DNA assembly of long uncorrected reads

SYNPOPSIS

       racon [options ...] <sequences> <overlaps> <target sequences>

DESCRIPTION

       Racon  is  intended  as  a standalone consensus module to correct raw contigs generated by rapid assembly
       methods which do not include a consensus step. The goal of Racon is to generate genomic  consensus  which
       is  of  similar  or better quality compared to the output generated by assembly methods which employ both
       error correction and consensus steps, while providing a  speedup  of  several  times  compared  to  those
       methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.

       Racon  can  be  used as a polishing tool after the assembly with either Illumina data or data produced by
       third generation of sequencing. The type of data inputed is automatically detected.

       Racon takes as input only three files: contigs in FASTA/FASTQ format, reads  in  FASTA/FASTQ  format  and
       overlaps/alignments between the reads and the contigs in MHAP/PAF/SAM format. Output is a set of polished
       contigs in FASTA format printed to stdout. All input files can be compressed with gzip.

       Racon can also be used as a read error-correction tool. In this scenario, the MHAP/PAF/SAM file needs  to
       contain pairwise overlaps between reads including dual overlaps.

       A wrapper script is also available to enable easier usage to the end- user for large datasets. It has the
       same interface as racon but adds two additional features from the outside. Sequences can be subsampled to
       decrease  the  total  execution  time  (accuracy might be lower) while target sequences can be split into
       smaller chunks and run sequentially to decrease memory consumption. Both features can be run at the  same
       time as well.

OPTIONS

       <sequences>

              input  file  in  FASTA/FASTQ  format  (can  be compressed with gzip) containing sequences used for
              correction

       <overlaps>

              input file in MHAP/PAF/SAM format (can  be  compressed  with  gzip)  containing  overlaps  between
              sequences and target sequences

       <target sequences>

              input  file in FASTA/FASTQ format (can be compressed with gzip) containing sequences which will be
              corrected

   optional
       -u, --include-unpolished

              output unpolished target sequences

       -f, --fragment-correction

              perform fragment correction instead of contig polishing (overlaps file  should  contain  dual/self
              overlaps!)

       -w, --window-length <int>

              default: 500 size of window on which POA is performed

       -q, --quality-threshold <float>

              default: 10.0 threshold for average base quality of windows used in POA

       -e, --error-threshold <float>

              default: 0.3 maximum allowed error rate used for filtering overlaps

       -m, --match <int>

              default: 5 score for matching bases

       -x, --mismatch <int>

              default: -4 score for mismatching bases

       -g, --gap <int>

              default: -8 gap penalty (must be negative)

       -t, --threads <int>

              default: 1 number of threads

       --version

              prints the version number

       -h, --help

              prints the usage

AUTHOR

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