💠Pipeline Logic

Descriptions of the logic underlying the DRAGEN Targeted Microbial analysis pipeline

Flowchart

Pipeline Steps

StepModule/ScriptRun

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

StatusLevelOutcomeOutput 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)

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