metagenomics-nf

Nextflow pipeline to perform metagenomic analyses from next-generation sequncing data

Description

Nextflow pipeline running software centrifuge to detect reads mapping to microbial or viral references, and optionally software virusbreakend to detect viral integration

Dependencies

1. This pipeline is based on nextflow. As we have several nextflow pipelines, we have centralized the common information in the IARC-nf repository. Please read it carefully as it contains essential information for the installation, basic usage and configuration of nextflow and our pipelines.
2. External software:

• centrifuge
• samtools
• virusbreakend

You can avoid installing all the external software by only installing Docker. See the IARC-nf repository for more information.

To use virusbreakend, you will need to download the database. See help at https://github.com/PapenfussLab/gridss/blob/master/VIRUSBreakend_Readme.md

Input

Type	Description
input_folder	Input folder with BAM or CRAM files

Parameters

• Optional

Name	Default value	Description
--output_folder		metagenomics-nf_results
--cpu	2	Number of CPUs
--mem	8	Memory in Gb
--ref		Host reference genome
--virusbreakend_db		Virusbreakend database (e.g., virusbreakenddb_20210401 from https://github.com/PapenfussLab/gridss/blob/master/VIRUSBreakend_Readme.md)

• Flags

Flags are special parameters without value. The virusbreakend process will be triggered automatically if the virusbreakend_db parameter is specified.

Name	Description
--help	Display help

Usage

nextflow run iarcbioinfo/metagenomics-nf --input_folder crams

Output

Type	Description
*_centrifuge_report.tsv	Centrifuge summary reports per sample
*_centrifuge_results.txt	Centrifuge output per sample
*virusbreakend.vcf	Virusbreakend vcf file output

Contributions

Name	Email	Description
Nicolas Alcala*	alcalan@iarc.who.int	Developer to contact for support

References

Kim D, Song L, Breitwieser FP, and Salzberg SL. Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Research 2016