abacas - Algorithm Based Automatic Contiguation of Assembled Sequences
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
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.
ABACAS IS Copyright (C) 2008-10 The Wellcome Trust Sanger Institute, Cambridge,
UK.
This manual page was written by Andreas Tille <
[email protected]>, for the
Debian project (and may be used by others).