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ABACAS2, a tool for ordering and orientating biosequences along a reference
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ABACAS2 is a tool to order and orientate a set of input sequences along a reference sequence, based on high confidence local alignments as generated by MUMmer.

Software dependencies

  • Perl 5
  • MUMmer version 3
  • NCBI BLAST (needs blastall)


To run ABACAS2, just clone this repo into a directory of your choosing and make sure all dependencies are installed and available in your $PATH. Also, please make sure that the ABACAS2 installation directory is both in $PATH and $PERL5LIB:

export PERL5LIB=<installation directory>:$PERL5LIB
export PATH=<installation directory>:$PATH

(example for bash)

Running ABACAS2

Usage: <reference> <Contig to order> <min aligment length> <Identity cutoff> <doblast: 0/1>

reference:           Fasta (or multi-fasta) against which the 
                     contigs should be ordered
contig:              Contigs or query that should be ordered
Min aligment length: Alignment length significance threshold (default 200)
Identity cutoff:     Threshold for identity to place contigs (default 95)
Do Blast:            Does a BLAST run for ACT inspection (default 0)

The options for min alignment length, identity cutoff and doblast are optional.

###Results Results are all files beginning with Res.* -- this includes GFF files for contig placements, coverage plots to be loaded into Artemis, FASTA sequences for each contiguated pseudochromosome and the Res.abacasBin.fna file for all input sequences that could not be mapped to the reference (the 'bin').


ABACAS2 is released under GPL3.

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