Abacas - Revision history

Rf at 14:52, 7 June 2016

2016-06-07T14:52:11Z

Rf at 12:30, 7 June 2016

2016-06-07T12:30:10Z

Rf at 12:29, 7 June 2016

2016-06-07T12:29:31Z

Rf at 11:16, 7 June 2016

2016-06-07T11:16:12Z

Rf: Created page with "=Introduction= algorithm-based automatic contiguation of assembled sequences = Basic usage = First, load the software module load abacas Then, make a folder with the refe..."

2016-06-07T11:15:34Z

Created page with "=Introduction= algorithm-based automatic contiguation of assembled sequences = Basic usage = First, load the software module load abacas Then, make a folder with the refe..."

New page

=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

@@ Line 24: / Line 24: @@
 == 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

@@ Line 22: / Line 22: @@
   abacas.pl -h
-== Regular output == > abacas -q 454AllContigs.fna -r SS_SC84.dna -p nucmer
+== Regular output ==
   ***********************************************************************************
@@ Line 71: / Line 74: @@
                   Gaps in pseudomolecule are in: 454AllContigs.fna_SS_SC84.dna.gaps

← Older revision		Revision as of 12:29, 7 June 2016
Line 21:		Line 21:

	abacas.pl -h		abacas.pl -h
		+
		+	== Regular output == > 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
		+
		+
		+	This is what a proper run should look like:

@@ Line 8: / Line 8: @@
   module load abacas
-Then, make a folder with the reference seuqence and a multifasta file with the contigs.
+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: