SEQCONS(1)

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).