Data File Requirements

CZ ID supports short- and long-read data from Illumina and Nanopore sequencing platforms. To keep CZ ID's system available for all the users, we recommend limiting uploads (runs) to 500 samples per upload and not more than 1000 samples per week. Below we summarize file requirements for Illumina and Nanopore sequencing data. 

• Short-read (Illumina) sequencing files:
  • • The mNGS Illumina pipeline accepts sequence data in FASTQ format
      • Click here if you need to upload FASTA files.
    • CZ ID's Web App is limited to files < 35 GB. 
      • If you need to upload to upload files > 35 GB, consider the command line interface or subsampling.
    • Files should contain no less than 70 reads and read lengths less than 50 base pairs or more than 500 base pairs are not supported.
    • If uploading paired-end reads, the read length should be the same for both ends.
    • FASTQ files from multiple lanes associated with one given sample will be automatically concatenated during upload.
• Long-read (Nanopore) sequencing files:
  • • The mNGS Nanopore pipeline accepts FASTQ sequencing files.
      • Click here if you need to upload FASTA files.
    • CZ ID's Web App is limited to files < 35 GB. 
      • If you need to upload to upload files > 35 GB, consider the command line interface or subsampling.
    • Multiple FASTQ files for a given sample will be automatically concatenated if filenames follow a certain format (see Automatic Concatenation of Nanopore Files for details). 
    • If there are multiple FASTQ files per sample and filenames do not follow the format recognized by the platform, you need to concatenate into a single file before upload.