Abacas

Introduction

algorithm-based automatic contiguation of assembled sequences

Basic usage

First, load the software

module load abacas

Then, make a folder with the reference seuqence and a multifasta file with the contigs.

When wanting to order contigs and design primers, the format of the commmand is:

abacas -r <reference file: single fasta> -q <query sequence file: fasta> -p <nucmer/promer> [Options]

If ordering contigs is not required, this can be skipped so that primer design is the only task:

abacas.pl -r <reference file: single fasta> -q <pseudomolecule/ordered file: fasta> -e

In any case the following also gives help instructions:

abacas.pl -h