| Step | Module/Script | Run |
|---|---|---|
| Status | Level | Outcome | Output files (excluding log files) |
|---|---|---|---|
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
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)