Key Considerations when Uploading Sequencing Data (FASTQ)

Workflow Compatibility

• Shotgun Metagenomics profiling workflows supports paired-end sequencing data only from both short- and long-read sequencing technologies.
• Amplicon (16S, ITS) pipelines can accept single- and paired-end reads

File Size Limit and Formats

• Sequencing data files must not exceed 50 GB for shotgun sequencing data and 1 GB for ITS/16S sequencing data (250 MB when compressed in .gz).
• Supported File Formats: .fasta, .fasta.gz, .fas, .fas.gz, .fa, .fa.gz, .fsa, .fsa.gz, .fastq, .fastq.gz, .fna, .fna.gz, .seq, .seq.gz, .fq, .fq.gz, .bam, .bam.gz, .sra, .sra.gz (SRA files can be uploaded without extension).

Paired-End Data File Matching

Each sample ID requires two corresponding paired-end FASTQ files. Files should follow one of the acceptable naming conventions:

• <SampleID>_R1.fastq.gz and <SampleID>_R2.fastq.gz
• <SampleID>_R1_001.fastq.gz and <SampleID>_R2_001.fastq.gz

Naming Conventions

File names must not contain spaces or special characters. Only underscores (_), dashes (-), and alphanumeric characters are permitted.

Quality Requirements

All reads within FASTQ files must maintain an average base quality score greater than PHRED 20. This ensures optimal results from analysis pipelines.