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 sequence 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

Regular output

This is what a proper run should look like (acutally this is quite verbose, you may not get all this information, alot of it is output by MUMmer):

> abacas -q 454AllContigs.fna -r SS_SC84.dna -p nucmer

***********************************************************************************
* ABACAS: Algorithm Based Automatic Contiguation of Assembled Sequences           *
*                                                                                 *
*                                                                                 *
*   Copyright (C) 2008-10 The Wellcome Trust Sanger Institute, Cambridge, UK.     *
*   All Rights Reserved.                                                          *
*                                                                                 *
***********************************************************************************

#  Checking user options:
#       -r Reference=SS_SC84.dna
#       -q Query=454AllContigs.fna
#       -p nucmer
#       -d 0 use sensitive mapping in nucmer i.e. --maxmatch
#       Input checking done!!
PREPARING DATA FOR   nucmer 
1: PREPARING DATA
2,3: RUNNING mummer AND CREATING CLUSTERS
# reading input file "nucmer.ntref" of length 2095899
# construct suffix tree for sequence of length 2095899
# (maximum reference length is 536870908)
# (maximum query length is 4294967295)
# process 20958 characters per dot
#....................................................................................................
# CONSTRUCTIONTIME /usr/bin/mummer nucmer.ntref 0.53
# reading input file "/mnt/lvol0/nutriaDownloads/abacastest/454AllContigs.fna" of length 2071881
# matching query-file "/mnt/lvol0/nutriaDownloads/abacastest/454AllContigs.fna"
# against subject-file "nucmer.ntref"
# COMPLETETIME /usr/bin/mummer nucmer.ntref 2.14
# SPACE /usr/bin/mummer nucmer.ntref 4.05
4: FINISHING DATA
nucmer --maxmatch -l 12 -p nucmer SS_SC84.dna 454AllContigs.fna &> /dev/null
delta-filter -q nucmer.delta >nucmer.filtered.delta
show-tiling -i 40 -v 40 -V 1 -l 1 -R -u unused_contigs.out nucmer.filtered.delta > nucmer.tiling
Total contigs = 128 
 FINISHED CONTIG ORDERING

To view your results in ACT
                 Sequence file 1: SS_SC84.dna
                 Comparison file 1: 454AllContigs.fna_SS_SC84.dna.crunch
                 Sequence file 2: 454AllContigs.fna_SS_SC84.dna.fasta

                ACT feature file is: 454AllContigs.fna_SS_SC84.dna.tab

                Contigs bin file is: 454AllContigs.fna_SS_SC84.dna.bin

                Gaps in pseudomolecule are in: 454AllContigs.fna_SS_SC84.dna.gaps