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Omics Data Format

Omics Data Format

The data format that can be analyzed online are:

  • Pair-end FASTQ files, with suffixes of _R1.fastq.gz and _R2.fastq.gz or _R1.fq.gz and _R2.fq.gz.

  • unzipped VCF files, with suffixes of .vcf.

We suggest to standardize the file names of updated data files as follows:

Quartet_Omics_SequencePlatform_SequenceMachine_LibraryPrep_SequenceSite_Sample_Replicate_Date_R1/R2.fastq/fq.gz

Here are some examples of file names:

Fastq read 1: Quartet_WGS_ILM_Nova_PCRfree_FD_D5_1_20230635_R1.fq.gz

Fastq read 2: Quartet_WGS_ILM_Nova_PCRfree_FD_D5_1_20230635_R2.fq.gz

VCF:  Quartet_WGS_ILM_Nova_PCRfree_FD_D5_1_20230635.vcf

Fields in the file name are explained as follows:

  1. Omics

    Omics type Character
    DNA WGS WGS
    DNA WES WES

  2. SequencePlatform

    Platform Character
    illumina ILM
    BGI BGI
    Pacbio Pacbio
    Nanopore ONT

    Please note that the table provides examples of commonly used representative sequencing platforms, rather than an exhaustive compilation of all exiting sequencing platforms. If you use sequencing platforms not listed in the table, please use 2 to 6 letters as abbreviations to represent the sequencing platforms.

  3. SequenceMachine

    Platform Machine Character
    illumina XTen XTen
    illumina Novasq Nova
    illumina Hiseq4000 Hiseq4000
    illumina Hiseq2500 Hiseq2500
    illumina 10x 10x
    BGI SEQ500 SEQ500
    BGI SEQ2000 SEQ2000
    BGI DNBSEQ-T7 T7
    Pacbio Sequel Sequel
    Pacbio Sequel II Sequel2
    Nanopore PromethION 24 P24
    Nanopore MinION MinION

    Please note that the table provides examples of commonly used representative sequencing machines, rather than an exhaustive compilation of all exiting sequencing machines. If you use sequencing platforms not listed in the table, please use 2 to 6 letters as abbreviations to represent the sequencing machines.

  4. LibraryPrep

    LibraryPrep Character
    PCR PCR
    PCR-free PCRfree

  5. SequenceSite

    Please use a few uppercase letters as abbreviations to represent the sequence centers or labs. For example, Fudan to FD.

  6. Sample

    Sample Character
    Quartet-D5 D5
    Quartet-D6 D6
    Quartet-F7 F7
    Quartet-M8 M8

  7. Replicate

    If you sequenced multiple replicates for the same reference material, use numbers such as 1, 2, 3, ... to represent technical replicates.

  8. Date

    The format of Date is yyyymmdd. For example, June 25, 2023 shoud be written to 20230625.

Note

In addition, there is one thing to note when using the Quartet DNAseq APP. The "Sample ID" in the parameter setting page refers to the number of data sets (one technical replicate of each sample is considered as one set, i.e. D5-D6-F7-M8).

For example, if you provide data for 8 samples, that means two sets of data, so fill in "2".

Last update: 2023-06-20
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