Instructions For Use
Inputs: Reference Genome (FASTA) & Contigs (FASTA)
- Download ABACAS from the download page
- Run: perl abacas.pl -r <reference> -q
<contigs> -p <nucmer|promer>
NOTE: If ABACAS cannot find MUMmer from
the default path - it will prompt the user to enter the location of
MUMer
- ABACAS may take several minutes to run for large
genomes/chromosomes and will produce a number of different output files
in the working directory
- Start ACT
and load the sequence and comparison files as printed out by ABACAS.
- In ACT, load the contig names by going to 'File',
<query>, 'Read an Entry', and select the file
<query>_<reference>.tab
- You can also load the repeat plot for the reference which
tells whether or not gaps are due to repetitive sequence. You can load
this by going to 'Graph', '<reference>', 'Add User Plot',
and select the file '<reference>.Repeats.plot'
- The file '<query>.bin' contains the names of
the contigs that were not mapped and mapped multiple times to the
reference.
A detailed documentation and test dataset could be found in the
user manual page.
Conact
Email: sa4 {at} sanger.ac.uk
