💠Pipeline Logic

Descriptions of the logic underlying the DRAGEN Targeted Microbial analysis pipeline

Flowchart

Control and data flow diagram for the DRAGEN Targeted Microbial analysis pipeline

Pipeline Steps

Step	Module/Script	Run
Reference reformatting/validation	custom script	If custom reference is provided
Read QC	trimmomatic	Always
Primer trimming (on FASTQ)	trimmomatic	If primer set exists
Read dehosting	human_read_scrubber	If checked in Input Form
Assembly	MEGAHIT	If reference FASTA and BED files imply more than one genome as reference
Contig clustering	CD-HIT	If assembly ran
Reference selection	custom script	If assembly ran, otherwise input reference database is used as is
Primer alignment / reformatting	custom script	If primer set is provided. Primers are aligned to selected reference sequences if coordinates are not provided. Otherwise, primers mapping to selected reference sequences (based on the provided primer coordinates) are selected as final set of primers
Map/Align	DRAGEN	If at least one reference sequence is generated
Post-facto primer trimming (on BAM)	custom script	If Map/Align ran and primer set exists
Sample filtering based on amplicon coverage	custom script	If Map/Align ran and primer set exists
Variant calling	DRAGEN	If Map/Align ran and sample passed filter above
Consensus sequence generation	custom script	If Map/Align ran and sample passed filter above

Possible outcomes

Status	Level	Outcome	Output files (excluding log files)
Pipeline completed	Pipeline	Pipeline exits	All
Custom files are not formatted correctly	Pipeline	Pipeline exits	None
None of the primers provided in custom primer definition file align to selected reference sequences	Sample	Skip post-factor primer trimming and sample filtering based on amplicon coverage for this sample	All except for amplicon-related output files
No reference found after assembly	Sample	Do not proceed to short read map alignment for this sample	Contig FASTA
Insufficient amplicon coverage	Sample	Do not proceed to variant calling for this sample	Contig FASTA (if assembly was run)