Difference between revisions of "Abacas"
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== Regular output == | == Regular output == | ||
− | This is what a proper run should look like: | + | 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 -q 454AllContigs.fna -r SS_SC84.dna -p nucmer | ||
Latest revision as of 14:52, 7 June 2016
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