BCL Convert software output files

BCL-convert was initially included in the DRAGEN Suite and greatly reduces the overall time needed to convert BCL files to FASTQ files with the FPGA hardware acceleration. Starting 28-JUL-2020, BCL convert has been released as a stand-alone software and has parity to the BCL convert included with DRAGEN 3.6.3 and above version

Output files

The following files are created in the /Reports/. Detailed Information can be found in the bcl convert user guide.

Columns (if applicable) of the files included below.

• Adapter_Metrics.csv

  • 

• Demultiplex_Stats.csv

  • 
• fastq_list.csv

  • This file that can be used for DRAGEN analysis and contains the file path and information to input a single Sample for downstream analysis. (Note: using a single FASTQ file list will not batch launch all samples present. Rather, if --fastq-list-all-samples true is used, it will merge all sample information into a single dataset.)

  • RGID

  • RGSM

  • Lane

  • Read1File

  • Read2File

• Index_Hopping_Counts.csv

  • *Only applicable when Unique Dual Indexes (UDIs) are used, otherwise the file will output a header-only file

• IndexMetricsOut.bin

  • Binary file to be used with SAV

• RunInfo.xml

• SampleSheet.csv

• Top_Unknown_Barcodes.csv

  • 

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