NAME

       abacas - Algorithm Based Automatic Contiguation of Assembled Sequences

SYNOPSIS

       abacas -r ref -q qs -p prog  [OPTIONS]

       OR

       abacas -r ref -q psf -e

       ref    reference sequence in a single fasta file

       qs     contigs in multi-fasta format

       rog    MUMmer program to use: 'nucmer' or 'promer'

       psf    pseudomolecule/ordered sequence file in fasta format

       OPTIONS

       -h     print usage

       -d     use default nucmer/promer parameters

       -s     int     minimum length of exact matching word (nucmer default = 12, promer  default
              = 4)

       -m     print ordered contigs to file in multifasta format

       -b     print contigs in bin to file

       -N     print a pseudomolecule without "N"s

       -i     int     mimimum percent identity [default 40]

       -v     int     mimimum contig coverage [default 40]

       -V     int     minimum contig coverage difference [default 1]

       -l     int     minimum contig length [default 1]

       -t     run tblastx on contigs that are not mapped

       -g     string (file name)      print uncovered regions (gaps) on reference to file name

       -a     append contigs in bin to the pseudomolecule

       -o     prefix  output files will have this prefix

       -P     pick primer sets to close gaps

       -f     int     number of flanking bases on either side of a gap for primer design (default
              350)

       -R     int     Run mummer [default 1, use -R 0 to avoid running mummer]

       -e     Escape contig ordering i.e. go to primer design

       -c     Reference sequence is circular

DESCRIPTION

       ABACAS is intended to rapidly contiguate (align, order, orientate), visualize  and  design
       primers to close gaps on shotgun assembled contigs based on a reference sequence.

       ABACAS uses MUMmer to find alignment positions and identify syntenies of assembled contigs
       against the reference. The output is then processed to generate  a  pseudomolecule  taking
       overlapping  contigs  and gaps in to account. ABACAS generates a comparision file that can
       be used to visualize ordered and oriented contigs in ACT. Synteny is  represented  by  red
       bars  where  colour  intensity  decreases  with  lower  values of percent identity between
       comparable blocks. Information on contigs  such  as  the  orientation,  percent  identity,
       coverage  and  overlap  with other contigs can also be visualized by loading the outputted
       feature file on ACT.

AUTHOR

       ABACAS IS Copyright (C) 2008-10 The Wellcome Trust Sanger Institute, Cambridge, UK.

       This manual page was written by Andreas Tille <tille@debian.org>, for the  Debian  project
       (and may be used by others).