Instructions For Use

Inputs: Reference Genome (FASTA) & Contigs (FASTA)
  1. Download ABACAS from the download page
  2. Run: perl -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
  3. ABACAS may take several minutes to run for large genomes/chromosomes and will produce a number of different output files in the working directory
  4. Start ACT and load the sequence and comparison files as printed out by ABACAS.
  5. In ACT, load the contig names by going to 'File', <query>, 'Read an Entry', and select the file <query>_<reference>.tab
  6. 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'
  7. The file '<query>.bin' contains the names of the contigs that were not mapped and mapped multiple times to the reference.

User manual

A detailed documentation and test dataset could be found in the user manual page.


Email: sa4 {at} 

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