Running DRAGEN analyses with ORA files as input

DRAGEN ORA files can be used directly as input for the map/align step or they can be decompressed to FastQ files first. Here are a few scenarios which use ORA files as input and the flags that need to be included in said analyses.

Input	Map/Align	FastQ Output	Flags to be used
ORA	Yes	No	--ora-reference [path to the ORA reference] --enable-map-align true | ORA | No | Yes | --ora-reference [path to the ORA reference] --enable-map-align true
--ora-reference [path to the ORA reference] --enable-map-align true
--ora-reference [path to the ORA reference] --enable-map-align true
ORA	No	Yes	--ora-reference [path to the ORA reference] --enable-ora true --ora-decompress true --enable-map-align false | | ORA | Yes | Yes | --ora-reference [path to the ORA reference] --enable-ora true --ora-decompress true --enable-map-align false
--ora-reference [path to the ORA reference] --enable-ora true --ora-decompress true --enable-map-align false
--ora-reference [path to the ORA reference] --enable-ora true --ora-decompress true --enable-map-align false
ORA	Yes	Yes	--ora-reference [path to the ORA reference] --enable-ora true --ora-decompress true --enable-map-align true | More information about ORA compression/decompression can be found in the user guide. For any feedback or questions regarding this article (Illumina Knowledge Article #7955), contact Illumina Technical Support [e-mail].
--ora-reference [path to the ORA reference] --enable-ora true --ora-decompress true --enable-map-align true
For any feedback or questions regarding this article (Illumina Knowledge Article #7955), contact Illumina Technical Support [e-mail].