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Requirements for submitted FASTQ files

VarSome Clinical accepts FASTQ files from Illumina, MGI, Element Biosciences, or GeneMind sequencers and expects that the files conform to the respective naming conventions of those manufacturers.  

When providing paired-end FASTQ files, we require that the reads are properly coordinated between them. Paired-end reads provided in a single FASTQ file are not accepted.

Additionally, FASTQ files need to be trimmed, with adapter content removed, before uploading to VarSome clinical.

For Illumina and Element Biosciences paired-end files, we will consider pairs to be files with the same name except for the number of the read.

For example:

  • SampleName_S1_L001_R1_001.fastq.gz and

  • SampleName_S1_L001_R2_001.fastq.gz.


We accept files in which the read number is specified alone:

  • For example SN1234_S1_L001_1.fastq.gz and SN1234_S1_L001_2.fastq.gz 

or with an “R” before the number:

  • For example SN5678_S1_L001_R2.fastq.gz and SN5678_S1_L001_R1.fastq.gz.

For further instructions in terms of naming conventions, please refer to Illumina. 

 

For MGI paired-end files, we will parse the files as follows:

  • [flow cell ID]_[lane ID]_[barcode ID]_(optional_id)_[read 1/2].fastq.gz

and we accept the number of the read to be specified alone:

  • For example, 12345_L02_48_1.fastq.gz and 12345_L02_48_2.fastq.gz 

or with an “R” before the number:

  • For example, 6789_L02_56_R1.fastq.gz and 6789_L02_56_R2.fastq.gz

For further instructions in terms of naming conventions, please refer to MGI Tech. 


In cases were there are more than two paired-end files per sample, all the paired reads should have the following naming structure: 

E12345_34_4321_L001_R1_001.fastq.gz 
E12345_34_4321_L001_R2_001.fastq.gz
E12345_34_4321_L002_R1_001.fastq.gz
E12345_34_4321_L002_R2_001.fastq.gz
E12345_34_4321_L003_R1_001.fastq.gz
E12345_34_4321_L003_R2_001.fastq.gz