https://github.com/maxibor/kraken-nf
Simple Kraken2 Nextflow pipeline
https://github.com/maxibor/kraken-nf
Last synced: 5 months ago
JSON representation
Simple Kraken2 Nextflow pipeline
- Host: GitHub
- URL: https://github.com/maxibor/kraken-nf
- Owner: maxibor
- License: gpl-3.0
- Created: 2019-07-10T12:29:54.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2021-12-02T15:55:29.000Z (over 4 years ago)
- Last Synced: 2025-12-17T09:42:43.923Z (6 months ago)
- Language: Nextflow
- Size: 29.9 MB
- Stars: 5
- Watchers: 0
- Forks: 3
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
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# Kraken-nf
Simple [Kraken2](https://github.com/DerrickWood/kraken2)/[Bracken](https://github.com/jenniferlu717/Bracken) Nextflow pipeline
## Dependancies
- [conda](https://conda.io/en/latest/)
- [Nextflow](https://www.nextflow.io/) : `conda install -c bioconda nextflow`
## Usage
```
nextflow run maxibor/kraken-nf --reads "/path/to/paired_end_reads_*.{1,2}.fastq.gz" --krakendb "/path/to/minikraken2_v2_8GB_201904_UPDATE.tgz"
```
### Input
#### --reads
Use this to specify the location of your input FastQ files. For example:
`--reads 'path/to/data/sample_*_{1,2}.fastq'`
**Please note the following requirements:**
- The path must be enclosed in quotes
- The path must have at least one \* wildcard character
- When using the pipeline with paired end data, the path must use {1,2} notation to specify read pairs.
#### --krakendb
Path to Kraken2 MiniKraken2_v2_8GB Database. A pre-build database can be downloaded [here](https://benlangmead.github.io/aws-indexes/k2)
#### --kraken_mem
Amount of memory allocated to Kraken2.
Depends on the kraken database.
Example:
```bash
--kraken_mem '9G'
```
## Kraken2 database
Any Kraken2 database can be used, but the _PlusPFP-8_ is a good compromise between speed and accuracy.
Please have a look at the [Index zone](https://benlangmead.github.io/aws-indexes/k2) to download it.
## Help
```
$ nextflow run maxibor/kraken-nf --help
N E X T F L O W ~ version 21.04.0
kraken-nf: simple Kraken2/Bracken Nextflow pipeline
Homepage: https://github.com/maxibor/kraken-nf
Author: Maxime Borry
=========================================
Usage:
The typical command for running the pipeline is as follows:
nextflow run maxibor/kraken-nf --reads '/path/to/paired_end_reads_*.{1,2}.fastq.gz' --krakendb '/path/to/minikraken2_v2_8GB_201904_UPDATE.tgz'
Mandatory arguments:
--reads Path to input data (must be surrounded with quotes)
--krakendb Path to MiniKraken2_v2_8GB Database
--kraken_mem Memory allocated to kraken2. Ex: '4G'. Default to 9G
Settings:
--minimum_read_length Minimum read length to keep. Default to null
--minhit Minimum number of Kraken hits to report Taxonomic level. Defaults to 10
--phred Specifies the fastq quality encoding (33 | 64). Defaults to 33
--pairedEnd Specified if reads are paired-end (true | false). Default = true
--build_bracken_db Build Bracken database (true | false). Default = false
--run_bracken Run Bracken (true | false). Default = true
--bracken_level Specifies the taxonomic level for Bracken. Default = S
--bracken_threshold Specifies the threshold for Bracken. Default = 10
Options:
--results The output directory where the results will be saved. Defaults to ./results
--help --h Shows this help page
```