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 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     minimum percent identity [default 40]

       -v     int     minimum 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 comparison 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).