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.
- Perl 5
- MUMmer version 3
- NCBI BLAST (needs
To run ABACAS2, just clone this repo into a directory of your choosing and make sure all dependencies are installed and available in your
$PATH. Also, please make sure that the ABACAS2 installation directory is both in
export PERL5LIB=<installation directory>:$PERL5LIB export PATH=<installation directory>:$PATH
(example for bash)
abacas2.nonparallel.sh <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 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.