NCBI_Scrub¶

Quick Facts¶

Workflow Type	Applicable Kingdom	Last Known Changes	Command-line Compatibility	Workflow Level
Standalone	Any Taxa	PHB v2.2.1	Yes	Sample-level

NCBI Scrub Workflows¶

NCBI Scrub, also known as the human read removal tool (HRRT), is based on the SRA Taxonomy Analysis Tool that will take as input a FASTQ file, and produce as output a FASTQ file in which all reads identified as potentially of human origin are either removed (default) or masked with 'N'. There are three Kraken2 workflows:

NCBI_Scrub_PE is compatible with Illumina paired-end data
NCBI_Scrub_SE is compatible with Illumina single-end data

Inputs¶

Terra Task Name	Variable	Type	Description	Default Value	Terra Status	Workflow
dehost_pe or dehost_se	read1	File			Required	PE, SE
dehost_pe or dehost_se	read2	File			Required	PE
dehost_pe or dehost_se	samplename	String			Required	PE, SE
dehost_pe or dehost_se	target_organism	String	Target organism for Kraken2 reporting	"Severe acute respiratory syndrome coronavirus 2"	Optional	PE, SE
kraken2	cpu	Int	Number of CPUs to allocate to the task	4	Optional	PE, SE
kraken2	disk_size	Int	Amount of storage (in GB) to allocate to the task. Increase this when using large (>30GB kraken2 databases such as the "k2_standard" database)	100	Optional	PE, SE
kraken2	docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/staphb/kraken2:2.0.8-beta_hv	Optional	PE, SE
kraken2	kraken2_db	String	The database used to run Kraken2	/kraken2-db	Optional	PE, SE
kraken2	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	PE, SE
kraken2	read2	File	Internal component, do not modify		Do not modify, Optional	SE
kraken2	target_organism	String	The organism whose abundance the user wants to check in their reads. This should be a proper taxonomic name recognized by the Kraken database.		Optional	PE, SE
ncbi_scrub_pe or ncbi_scrub_se	cpu	Int	Number of CPUs to allocate to the task	4	Optional	PE, SE
ncbi_scrub_pe or ncbi_scrub_se	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional	PE, SE
ncbi_scrub_pe or	docker	Int	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/ncbi/sra-human-scrubber:2.2.1	Optional	PE, SE
ncbi_scrub_pe or ncbi_scrub_se	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional	PE, SE
version_capture	docker	String	The Docker container to use for the task	"us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0"	Optional	PE, SE
version_capture	timezone	String	Set the time zone to get an accurate date of analysis (uses UTC by default)		Optional	PE, SE

Workflow Tasks¶

This workflow is composed of two tasks, one to dehost the input reads and another to screen the clean reads with kraken2 and the viral+human database.

ncbi_scrub: human read removal tool

Briefly, the HRRT employs a k-mer database constructed of k-mers from Eukaryota derived from all human RefSeq records and subtracts any k-mers found in non-Eukaryota RefSeq records. The remaining set of k-mers compose the database used to identify human reads by the removal tool.

Tool Name Technical Details

	Links
Task	task_ncbi_scrub.wdl
Software Source Code	HRRT on GitHub
Software Documentation	HRRT on NCBI

kraken2: taxonomic profiling

Kraken2 is a bioinformatics tool originally designed for metagenomic applications. It has additionally proven valuable for validating taxonomic assignments and checking contamination of single-species (e.g. bacterial isolate, eukaryotic isolate, viral isolate, etc.) whole genome sequence data.

Kraken2 is run on the set of raw reads, provided as input, as well as the set of clean reads that are resulted from the read_QC_trim workflow

Database-dependent

TheiaCoV automatically uses a viral-specific Kraken2 database.

Kraken2 Technical Details

	Links
Task	task_kraken2.wdl
Software Source Code	Kraken2 on GitHub
Software Documentation	https://github.com/DerrickWood/kraken2/wiki
Original Publication(s)	Improved metagenomic analysis with Kraken 2

Outputs¶

Variable	Type	Description	Workflow
kraken_human_dehosted	Float	Percent of human read data detected using the Kraken2 software after host removal	PE, SE
kraken_report_dehosted	File	Full Kraken report after host removal	PE, SE
kraken_sc2_dehosted	Float	Percent of SARS-CoV-2 read data detected using the Kraken2 software after host removal	PE, SE
kraken_version_dehosted	String	Version of Kraken2 software used	PE, SE
ncbi_scrub_docker	String	Docker image used to run HRRT	PE, SE
ncbi_scrub_human_spots_removed	Int	Number of spots removed (or masked)	PE, SE
ncbi_scrub_pe_analysis_date	String	Date of analysis	PE, SE
ncbi_scrub_pe_version	String	Version of HRRT software used	PE, SE
read1_dehosted	File	Dehosted forward reads	PE, SE
read2_dehosted	File	Dehosted reverse reads	PE