WORKFLOW: Metagenomics

The Metagenomics workflow can process and QC metagenomics or metatranscriptomics datasets and offers options for extended runtime and resources to handle the large datasets.

Parameter Identifier	Parameter Value Type / Default	Parameter Description
run_subsample	String/Boolean. False	Specify whether to perform subsampling of reads (e.g. to quickly get a glimpse of the data).
read_subsampling	Integer. 10000	The number of reads to subsample.
run_centrifuge	String/Boolean. True	Whether to run Centrifuge.
centrifuge_index	String.	Path to the Centrifuge database index.
centrifuge_threads	Integer. 1	The number of cores/threads to provide for Centrifuge.
centrifuge_memory	Integer. 32	The memory (in Gb per core/thread) to provide for Centrifuge.
trimgalore_options	String.	Options for TrimGalore for adapter trimming of FASTQs.
run_kneaddata	String/Boolean. True	Run kneaddata QC, including Trimmomatic quality trimming.
kneaddata_options	String. --reference-db /path/to/Homo_sapiens	Options to run kneaddata with. Currently used to specify path to reference database to be used for running contamination removal of host DNA.
kneaddata_threads	Integer. 1	The number of cores/threads to provide for kneaddata.
kneaddata_memory	Integer. 32	The memory (in Gb per core/thread) to provide for kneaddata.
run_metaphlan2	String/Boolean. True	Whether to run MetaPhlAn2 profiling.
metaphlan2_threads	Integer. 1	The number of cores/threads to provide for MetaPhlAn2.
run_sortmerna	String/Boolean. False	Whether to run SortMeRNA for rRNA depletion (for meta-transcriptomic datasets).
sortmerna_db	String.	Path to directory with SortMeRNA ribosomal RNA database files.
sortmerna_threads	Integer. 4	The number of cores/threads to provide for SortMeRNA.
sortmerna_memory	Integer. 16	The memory (in Gb per core/thread) to provide for SortMeRNA.
run_straingst	String/Boolean. False	Whether to run StrainGST analysis to find strains from a specific species.
straingst_db	String.	Path to StrainGST k-mer pan-genome database (*.hdf5 file).
run_shortbred	String/Boolean. False	Whether to run ShortBRED to find AMR genes in data.
amr_shortbred_markers	String.	Path to ShortBRED AMR markers database.
set_timelimit_sevendays	String/Boolean. False	Whether to change timelimit to 7 full days for intensive steps. Meant for large datasets.
run_cleanup	String/Boolean. False	Delete intermediate FASTQ files: True/False