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.