The primary goal of V(D)J analysis is to extract the V(D)J gene sequences and clonotypes of B cells or T cells from raw sequencing data. This process is typically adaptable to different sequencing platforms and data formats. Therefore, the V(D)J analysis pipeline does support FASTQ files from multiple sequencing platforms.

For example, at the data analysis level, V(D)J analysis software like IgBlast can handle FASTQ files from various sequencing platforms, including Illumina, BGI, and Ion Torrent. Similarly, MobiVision analysis software can process FASTQ files from different sequencing platforms. However, due to differences in read length and quality characteristics across platforms, these factors may need to be considered during V(D)J analysis.