BCL Data Conversion

The Illumina BCL Convert is a standalone local software application that converts the Binary Base Call (BCL) files produced by Illumina sequencing systems to FASTQ files. The DRAGEN product includes hardware accelerated BCL conversion on the DRAGEN platform, which results in improved run times compared to BCL Convert pure software execution.

The DRAGEN BCL conversion is designed to output FASTQ files that match bcl2fastq2 v2.20 output. DRAGEN supports direct conversion from .BCL to the compressed FASTQ.ORA format in order to reduce the FASTQ.GZ file size by a ratio up to 5. Refer to DRAGEN ORA compression from BCL for proper usage.

DRAGEN BCL Convert supports the following features.

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Demultiplexing samples by barcode with optional mismatch tolerance

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Supports adapter sequence masking or trimming with adjustable matching stringency.

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Supports UMI sequence tagging and optional trimming

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Optional Output of FASTQ files for index reads (in gzipped or FASTQ.ORA files)

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Optional Combines all lanes to the same FASTQ output files

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Supports high sample count (100,000)

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Supports UMI sequences in index reads

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Eliminates skew as the result of adapter sequence trimming by using the MinimumAdapterOverlap setting

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Outputs metrics for demultiplexing, quality scores, adapter trimming, unmapped barcodes, and index-hopping detection.

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Outputs per-cycle adapter metrics and per-tile quality & demultiplex metics

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Converts a subset of tiles specified by regular-expressions using an allow list, a block list, or both.

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Better support for legacy applications based upon bcl2fastq2 (all off by default):

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Output metrics in bcl2fastq2 Stats directory format in addition to csv

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Support FindAdaptersWithIndels setting to match bcl2fastq2 default output

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Support fastq subdirectories named by sample project, sampleID, & sampleName