FASTQ Format Compatibility

FASTQ is a common format for genome sequencing data. FASTQ files can be uploaded with any commonly used file extension, with or without compression:

• .fastq
• .fastq.gz
• .fq
• .fq.gz

If you received a FASTQ file from an exome or whole genome sequencing test, you can upload it directly through the Upload Center. For guidance on which sequencing files are most useful for apps and reports, see the guide for using genome sequencing data files.

Supported FASTQ Types

Paired FASTQ (recommended)

Most whole genome and exome sequencing results are provided as two FASTQ files called paired FASTQ files. This is the recommended format for upload.

The main part of the filename (before the extension) for both paired files must be exactly the same, except for the R1 and R2 designations. Some files may use 1 and 2 instead of R1 and R2, which is also fine.

• The file containing the forward sequence should include R1 or 1 in the filename. Examples: samplefastqfilename-R1.fastq.gz, samplefastqfilename-1.fastq.gz
• The file containing the reverse sequence should include R2 or 2 in the filename. Examples: samplefastqfilename-R2.fastq.gz, samplefastqfilename-2.fastq.gz

Multi-FASTQ

Some sequencing laboratories provide a genome as three or more FASTQ files. Multi-FASTQ genomes are supported through One Genome Technology, which automatically combines all FASTQ files for the same genome into a single digital genome.

If you have a multi-FASTQ genome and need assistance uploading it, contact support@sequencing.com.

FASTQ Types Not Compatible With Apps and Reports

The following FASTQ types are not compatible with DNA analysis apps and reports:

• Single read FASTQ - A single FASTQ file with only one read direction. This format lacks sufficient data for accurate analysis and may produce incorrect results.
• Concatenated FASTQ - A single file created by concatenating multiple FASTQ files without proper pairing. This is different from a standard single-read file and may cause processing errors.

If you received a single read or concatenated FASTQ, contact the laboratory that provided your data and request paired FASTQ files (two files with R1 and R2 designations). Paired FASTQ and single concatenate FASTQ are the most common formats generated by whole genome and exome sequencing for healthcare and consumer use.

If you are unable to obtain paired FASTQ files, a bioinformatician or genomics professional can concatenate the individual files into paired FASTQ. This is a complex task and should not be attempted without bioinformatics expertise.

If you have questions about which file format to upload, contact support@sequencing.com.