Shtsai at 00:16, 5 April 2026

2026-04-05T00:16:01Z

← Older revision		Revision as of 20:16, 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 ==
	3.1		3.1

	=== Author / Distributor ===		== Author / Distributor ==
	[https://github.com/jenniferlu717/Bracken Bracken]		[https://github.com/jenniferlu717/Bracken Bracken]

	=== Description ===		== Description ==
	"Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Braken uses the taxonomy labels assigned by Kraken, a highly accurate metagenomics classification algorithm, to estimate the number of reads originating from each species present in a sample. Kraken classifies reads to the best matching location in the taxonomic tree, but does not estimate abundances of species. We use the Kraken database itself to derive probabilities that describe how much sequence from each genome is identical to other genomes in the database, and combine this information with the assignments for a particular sample to estimate abundance at the species level, the genus level, or above. Combined with the Kraken classifier, Bracken produces accurate species- and genus-level abundance estimates even when a sample contains two or more near-identical species.		"Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Braken uses the taxonomy labels assigned by Kraken, a highly accurate metagenomics classification algorithm, to estimate the number of reads originating from each species present in a sample. Kraken classifies reads to the best matching location in the taxonomic tree, but does not estimate abundances of species. We use the Kraken database itself to derive probabilities that describe how much sequence from each genome is identical to other genomes in the database, and combine this information with the assignments for a particular sample to estimate abundance at the species level, the genus level, or above. Combined with the Kraken classifier, Bracken produces accurate species- and genus-level abundance estimates even when a sample contains two or more near-identical species.

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	More details are at [https://ccb.jhu.edu/software/bracken/ Bracken instructions]		More details are at [https://ccb.jhu.edu/software/bracken/ Bracken instructions]

	=== 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="gcommand">		<pre class="gcommand">
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	[[#top\|Back to Top]]		[[#top\|Back to Top]]

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

	source code from [https://github.com/jenniferlu717/Bracken Bracken]		source code from [https://github.com/jenniferlu717/Bracken Bracken]

	=== System ===		== System ==
	64-bit Linux		64-bit Linux

Jordan: Created this page to correspond to making the database files available in /db/Bracken/

2025-08-27T15:21:15Z

Created this page to correspond to making the database files available in /db/Bracken/

New page

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

Bioinformatics

=== Program On ===

Sapelo2

=== Version ===
3.1

=== Author / Distributor ===
[https://github.com/jenniferlu717/Bracken Bracken]

=== Description ===
"Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Braken uses the taxonomy labels assigned by Kraken, a highly accurate metagenomics classification algorithm, to estimate the number of reads originating from each species present in a sample. Kraken classifies reads to the best matching location in the taxonomic tree, but does not estimate abundances of species. We use the Kraken database itself to derive probabilities that describe how much sequence from each genome is identical to other genomes in the database, and combine this information with the assignments for a particular sample to estimate abundance at the species level, the genus level, or above. Combined with the Kraken classifier, Bracken produces accurate species- and genus-level abundance estimates even when a sample contains two or more near-identical species.

NOTE: Bracken is compatible with both Kraken 1 and Kraken 2. However, the default kmer length is different depending on the version of Kraken used. If you use Kraken 1 defaults, specify 31 as the kmer length. If you use Kraken 2 defaults, specify 35 as the kmer length."
More details are at [https://ccb.jhu.edu/software/bracken/ Bracken instructions]

=== Running Program ===

Also refer to [[Running Jobs on Sapelo2]]

We currently have the latest version of the following databases for Bracken available in /db/Bracken/20250827/:
<pre class="gcommand">
bacteria
core_nt
eupathdb
fungi
gtdb
pluspf
pluspfp
pluspfp-16
viral
</pre>
The bacteria database has been created for a read length of 100 (which is the default for Bracken), while the fungi and viral databases are for a read length of 150; all other databases can accommodate read lengths of 50, 75, 100, 150, 200, 250, and 300. Note, however, that only core_nt, eupathdb, gtdb, pluspf, pluspfp, and pluspfp-16 are also available for Kraken2 in /db/kraken2/20250814/.

Bracken analysis involves two steps, the first with Kraken 1 or 2 (Kraken2 is recommended as it involves only a single command and we also no longer have any Kraken1 databases available, so if you want to use Kraken1 you will need to acquire these for yourself) to generate a report file based on your FASTQ-formatted metagenomics sample, and the second with Bracken itself to estimate species- or other taxon-level abundances based on this report file. More detailed information can be found in the directions in the [https://github.com/jenniferlu717/Bracken#step-2-run-kraken-1-or-kraken-2-or-krakenuniq-and-generate-a-report-file GitHub] repository, bearing in mind that what you're doing is what the developers call "Step 2" and "Step 3" (their "Step 1" is to generate the Braken database files, but this isn't necessary because we already have them available).

'''Version 3.1'''

Version 3.1, installed at

* /apps/eb/Bracken/3.1-GCCcore-12.3.0/

To use it, please load the module with:
<div class="gscript2">
module load Bracken/3.1-GCCcore-12.3.0
</div>

Note that you need to load Kraken (if you use Kraken1 then you'll need to load it before you load Bracken, run the first step mentioned above, and then unload it before loading Bracken as we do not have Kraken1 installed with a compatible toolchain) and it's a good idea to load a toolchain-compatible version of Python (i.e., Python/3.11.3-GCCcore-12.3.0), as well.

Here is an example of a shell script sub.sh to run Bracken the batch partition using a read length of 150 and the PlusPF Kraken2/Bracken database:

<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash 
<nowiki>#</nowiki>SBATCH --job-name=BrackenJob 
<nowiki>#</nowiki>SBATCH --partition=batch 
<nowiki>#</nowiki>SBATCH --mail-type=ALL 
<nowiki>#</nowiki>SBATCH --mail-user=username@uga.edu 
<nowiki>#</nowiki>SBATCH --ntasks=1 
<nowiki>#</nowiki>SBATCH --cpus-per-task=4 
<nowiki>#</nowiki>SBATCH --mem100gb 
<nowiki>#</nowiki>SBATCH --time=08:00:00 
<nowiki>#</nowiki>SBATCH --output=log.%j.out 
<nowiki>#</nowiki>SBATCH --error=log.%j.err 

cd $SLURM_SUBMIT_DIR 

module load Bracken/3.1-GCCcore-12.3.0 
module load Kraken2/2.1.3-gompi-2023a 
module load Python/3.11.3-GCCcore-12.3.0 

<nowiki>#</nowiki>Do Step 1, where "SAMPLE.fastq" is the input file containing your metagenomics sequencing reads 
kraken2 --db /db/kraken2/20250814/pluspf --threads 4 --report SAMPLE.kreport SAMPLE.fastq > SAMPLE.kraken 
 
<nowiki>#</nowiki>Do Step 2 using the .kreport file generated in Step 1 as the input 
bracken -d /db/Bracken/20250827/pluspf -i ./SAMPLE.kreport -r 150 -o ./SAMPLE_150mers.bracken 
</div>

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values (make sure the value you use for "--cpus-per-task=" in the Slurm headers is the same as that used for "--threads" in the Kraken2 command)

Here is an example of job submission command:
<pre class="gcommand">
sbatch ./sub.sh
</pre>

=== Documentation ===

<pre class="gcommand">
$ module load Bracken/3.1-GCCcore-12.3.0
$ bracken -h
Usage: bracken -v -d MY_DB -i INPUT -o OUTPUT -w OUTREPORT -r READ_LEN -l LEVEL -t THRESHOLD
-v Echoes the current software version and exits
MY_DB location of Kraken database
INPUT Kraken REPORT file to use for abundance estimation
OUTPUT file name for Bracken default output
OUTREPORT New Kraken REPORT output file with Bracken read estimates
READ_LEN read length to get all classifications for (default: 100)
LEVEL level to estimate abundance at [options: D,P,C,O,F,G,S,S1,etc] (default: S)
THRESHOLD number of reads required PRIOR to abundance estimation to perform reestimation (default: 0)
</pre>
[[#top|Back to Top]]

=== Installation ===

source code from [https://github.com/jenniferlu717/Bracken Bracken]

=== System ===
64-bit Linux

Bracken-Sapelo2 - Revision history

Shtsai at 00:16, 5 April 2026

Jordan: Created this page to correspond to making the database files available in /db/Bracken/