Instructions For UseInputs: 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.
user manual page.