Racon-Sapelo2 - Revision history

Shtsai at 01:27, 5 April 2026

2026-04-05T01:27:27Z

← Older revision		Revision as of 21:27, 4 April 2026
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	[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
	=== Category ===		== Category ==

	Bioinformatics		Bioinformatics

	=== Program On ===		== Program On ==

	Sapelo2		Sapelo2

	=== Version ===		== Version ==

	1.5.0		1.5.0

	===Author / Distributor===		==Author / Distributor==

	Please see https://github.com/isovic/racon		Please see https://github.com/isovic/racon

	===Description===		==Description==

	From https://github.com/isovic/racon: Racon is a "Consensus module for raw de novo DNA assembly of long uncorrected reads. "		From https://github.com/isovic/racon: Racon is a "Consensus module for raw de novo DNA assembly of long uncorrected reads. "

	=== Running Program ===		== Running Program ==

	Also refer to [[Running Jobs on Sapelo2]]		Also refer to [[Running Jobs on Sapelo2]]
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	</pre>		</pre>

	=== Documentation ===		== Documentation ==
	<pre class="gscript">		<pre class="gscript">
	Please see links from https://github.com/isovic/racon.		Please see links from https://github.com/isovic/racon.
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	</pre>		</pre>

	=== Installation ===		== Installation ==

	Downloaded from https://github.com/lbcb-sci/racon/		Downloaded from https://github.com/lbcb-sci/racon/

	=== System ===		== System ==

	64-bit Linux		64-bit Linux

Chelsea: /* Version 1.5.0 */

2023-09-06T18:11:04Z

Version 1.5.0

← Older revision		Revision as of 14:11, 6 September 2023
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	=== Version ===		=== Version ===

	1.4.13		1.5.0

	===Author / Distributor===		===Author / Distributor===
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	For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.		For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.

	*Version 1.4.13, compiled with GCCcore/8.3.0 toolchain, installed in /apps/eb/Racon/1.4.13-GCCcore-8.3.0		*Version 1.5.0, compiled with GCCcore/11.2.0 toolchain, installed in /apps/eb/Racon/1.5.0-GCCcore-11.2.0

	To use this version of racon, please first load the module with		To use this version of racon, please first load the module with
	<pre class="gscript">		<pre class="gscript">
	ml Racon/1.4.13-GCCcore-8.3.0		ml Racon/1.5.0-GCCcore-11.2.0
	</pre>		</pre>
	'''Note:''' This version does not work on the nodes with AMD Opteron processors. You can request that your job does not get dispatched to a node with AMD Opteron processors by adding the following line to your job submission script:		'''Note:''' This version does not work on the nodes with AMD Opteron processors. You can request that your job does not get dispatched to a node with AMD Opteron processors by adding the following line to your job submission script:
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	cd $SLURM_SUBMIT_DIR		cd $SLURM_SUBMIT_DIR

	ml Racon/1.4.13-GCCcore-8.3.0		ml Racon/1.5.0-GCCcore-11.2.0

	racon -t 12 [options]		racon -t 12 [options]
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	Please see links from https://github.com/isovic/racon.		Please see links from https://github.com/isovic/racon.

	ml Racon/1.4.13-GCCcore-8.3.0		[cft07037@d2-13 all]$ ml Racon/1.5.0-GCCcore-11.2.0
			[cft07037@d2-13 all]$ racon -h
	racon -h
	usage: racon [options ...] <sequences> <overlaps> <target sequences>		usage: racon [options ...] <sequences> <overlaps> <target sequences>

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	-h, --help		-h, --help
	prints the usage		prints the usage

	</pre>		</pre>

Shtsai: /* Running Program */

2020-12-08T03:01:41Z

Running Program

← Older revision		Revision as of 23:01, 7 December 2020
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	For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.		For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.

	*Version 1.4.7, compiled with GCCcore/8.3.0 toolchain, installed in /apps/eb/Racon/1.4.13-GCCcore-8.3.0		*Version 1.4.13, compiled with GCCcore/8.3.0 toolchain, installed in /apps/eb/Racon/1.4.13-GCCcore-8.3.0

	To use this version of racon, please first load the module with		To use this version of racon, please first load the module with

Shtsai: Created page with "Category:Sapelo2Category:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 1.4.13 ===Author / Dist..."

2020-12-08T03:01:20Z

Created page with "Category:Sapelo2 Category:Software Category:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 1.4.13 ===Author / Dist..."

New page

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===

Bioinformatics

=== Program On ===

Sapelo2

=== Version ===

1.4.13

===Author / Distributor===

Please see https://github.com/isovic/racon

===Description===

From https://github.com/isovic/racon: Racon is a "Consensus module for raw de novo DNA assembly of long uncorrected reads. "

=== Running Program ===

Also refer to [[Running Jobs on Sapelo2]]

For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.

*Version 1.4.7, compiled with GCCcore/8.3.0 toolchain, installed in /apps/eb/Racon/1.4.13-GCCcore-8.3.0

To use this version of racon, please first load the module with
<pre class="gscript">
ml Racon/1.4.13-GCCcore-8.3.0
</pre>
'''Note:''' This version does not work on the nodes with AMD Opteron processors. You can request that your job does not get dispatched to a node with AMD Opteron processors by adding the following line to your job submission script:
<pre class="gscript">
#SBATCH --constraint=EDR
</pre>

Sample job submission script (sub.sh) to run racon 1.4.13 in a batch job:

<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=raconjob
#SBATCH --partition=batch
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=12
#SBATCH --constraint=EDR
#SBATCH --mem=20gb
#SBATCH --time=24:00:00
#SBATCH --output=%x.%j.out
#SBATCH --error=%x.%j.err

cd $SLURM_SUBMIT_DIR

ml Racon/1.4.13-GCCcore-8.3.0

racon -t 12 [options]
</pre>

where [options] need to be replaced by the options (command and arguments) you want to use. Other parameters of the job, such as the number of cores per node, the maximum wall clock time, the maximum memory, and the job name need to be modified appropriately as well. Note that if you use the racon option '''-t''' to specify using multi threads, please also request the same number of cores with '''--cpus-per-task'''. In the example above --cpus-per-task=12 and racon is invoked with -t 12.

Submit the job to the queue with
<pre class="gcommand">
sbatch sub.sh
</pre>

=== Documentation ===
<pre class="gscript">
Please see links from https://github.com/isovic/racon.

ml Racon/1.4.13-GCCcore-8.3.0

racon -h
usage: racon [options ...] <sequences> <overlaps> <target sequences>

#default output is stdout
<sequences>
input file in FASTA/FASTQ format (can be compressed with gzip)
containing sequences used for correction
<overlaps>
input file in MHAP/PAF/SAM format (can be compressed with gzip)
containing overlaps between sequences and target sequences
<target sequences>
input file in FASTA/FASTQ format (can be compressed with gzip)
containing sequences which will be corrected

options:
-u, --include-unpolished
output unpolished target sequences
-f, --fragment-correction
perform fragment correction instead of contig polishing
(overlaps file should contain dual/self overlaps!)
-w, --window-length <int>
default: 500
size of window on which POA is performed
-q, --quality-threshold <float>
default: 10.0
threshold for average base quality of windows used in POA
-e, --error-threshold <float>
default: 0.3
maximum allowed error rate used for filtering overlaps
--no-trimming
disables consensus trimming at window ends
-m, --match <int>
default: 3
score for matching bases
-x, --mismatch <int>
default: -5
score for mismatching bases
-g, --gap <int>
default: -4
gap penalty (must be negative)
-t, --threads <int>
default: 1
number of threads
--version
prints the version number
-h, --help
prints the usage

</pre>

=== Installation ===

Downloaded from https://github.com/lbcb-sci/racon/

=== System ===

64-bit Linux