VarSome Clinical accepts FASTQ files only from Illumina, MGI or Element Biosciences sequencers and expects that the files conform to Illumina's, MGI and Element Biosciences' naming convention.
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.
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