Difference between revisions of "Kraken"
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<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
| − | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | + | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |
|{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
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===Serial=== | ===Serial=== | ||
* {{#var:app}} | * {{#var:app}} | ||
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==System Variables== | ==System Variables== | ||
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
* HPC_{{uc:{{#var:app}}}}_BIN - executable directory | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory | ||
| + | * KRAKEN2_DB_PATH - directory with 'db' builds. | ||
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{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
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| + | After loading the kraken/2 module you can check the available databases with | ||
| + | $ ls $KRAKEN2_DB_PATH | ||
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| + | Use any of the standard or custom databases we host with the '-db DBNAME' argument. E.g. | ||
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| + | $ module load kraken/2 | ||
| + | $ kraken2-inspect -db fungi | ||
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|}} | |}} | ||
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Revision as of 18:18, 19 March 2021
Description
Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.
In its fastest mode of operation, for a simulated metagenome of 100 bp reads, Kraken processed over 4 million reads per minute on a single core, over 900 times faster than Megablast and over 11 times faster than the abundance estimation program MetaPhlAn. Kraken's accuracy is comparable with Megablast, with slightly lower sensitivity and very high precision.
Required Modules
Serial
- kraken
System Variables
- HPC_KRAKEN_DIR - installation directory
- HPC_KRAKEN_BIN - executable directory
- KRAKEN2_DB_PATH - directory with 'db' builds.
Additional Information
After loading the kraken/2 module you can check the available databases with
$ ls $KRAKEN2_DB_PATH
Use any of the standard or custom databases we host with the '-db DBNAME' argument. E.g.
$ module load kraken/2 $ kraken2-inspect -db fungi
Validation
- Validated 4/5/2018