Sequence File Formats

We provide numerous options for downstream analysis of sequence data and for converting the data to compatible sequence file formats. Sequencing systems are designed so data can be easily streamed into BaseSpace Sequence Hub for further analysis and collaboration.

For users interested in additional analysis options, raw data files are provided in sequence file formats that are compatible, or easily converted, for use with other software platforms.

The NextSeq, HiSeq, and NovaSeq Sequencing Systems generate raw data files in binary base call (BCL) format. This sequencing file format requires conversion to FASTQ format for use with user-developed or third-party data analysis tools.

Illumina offers bcl2fastq Conversion Software to convert BCL files. bcl2fastq is included, standalone conversion software that demultiplexes data and converts BCL files to standard FASTQ file formats for downstream analysis.

FASTQ is a text-based sequencing data file format that stores both raw sequence data and quality scores. FASTQ files have become the standard format for storing NGS data from Illumina sequencing systems, and can be used as input for a wide variety of secondary data analysis solutions.

The MiniSeq and MiSeq Sequencing Systems provide the option to automatically convert data from BCL to FASTQ format, so separate conversion software is not required.

FASTQ files are the starting format for data analysis; however, BaseSpace Sequence Hub can create file formats that are common to secondary and tertiary analysis programs.

During secondary or tertiary analysis of NGS data, software platforms and apps in the BaseSpace Informatics Suite will often convert raw sequence files from FASTQ files to other sequence file formats (ie, .vcf, .bam) as part of the analysis workflow.