NAME

       seqcons - Multi-read alignment

SYNOPSIS

       seqcons -r <FASTA file with reads> [Options]

DESCRIPTION

       Multi-read alignment - SeqCons

              seqcons -a <AMOS message file> [Options]

       -h,  --help
              displays this help message

       -V,  --version
              print version information

   Main Options:
       -r,  --reads <FASTA reads file>
              file with reads

       -a,  --afg <AMOS afg file>
              message file

       -o,  --outfile <Filename>
              output filename (default align.txt)

       -f,  --format [seqan | afg]
              output format (default afg)

       -m,  --method [realign | msa]
              alignment method (default realign)

       -b,  --bandwidth <Int>
              bandwidth (default 8)

       -n,  --noalign
              no align, only convert input

   MSA Method Options:
       -ma, --matchlength <Int>
              min. overlap length (default 15)

       -qu, --quality <Int>
              min. overlap precent identity (default 80)

       -ov, --overlaps <Int>
              min. number of overlaps per read (default 3)

       -wi, --window <Int>
              window size (default 0) /*If this parameter is > 0 then all

              overlaps within a given window are computed.*/

   ReAlign Method Options:
       -in, --include
              include contig sequence

       -rm, --rmethod [nw | gotoh]
              realign method (default gotoh)

AUTHOR

       seqcons was written by Tobias Rausch

       This  manual  page  was  generated  using  html2man  and  polished  by  Soeren  Sonnenburg
       <sonne@debian.org>, for the Debian project (but may be used by others).

Version 0.22 (06. August 2009) Revision: 4September 2009                               SEQCONS(1)