Pipeline Logic

Control and data flow diagram for the DRAGEN Microbial Amplicon app. Not all steps shown may be run depending on user inputs and pipeline outcome

Steps

Step	Module/Script	Run
QC	trimmomatic	Always
Primer trimming (on FASTQ)	trimmomatic	If assembly is to run
Remove off-target reads	DRAGEN	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
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

Outcomes

Status	Level	Outcome
Completed successfully	Pipeline	Exit with all applicable output files
Custom files are not formatted correctly	Pipeline	Exit early with error
No remaining reads after preprocessing	Sample	Exit early with a report of read counts
No contig generated	Sample	Exit early with a report of read counts
No reference found after assembly	Sample	Exit early with a report of read counts and contig FASTA
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
Insufficient amplicon coverage	Sample	Exit early before variant calling and consensus sequence generation