--- title: What are the input file requirements for the QC pipeline? description: We recommend between 0.5 and 2M paired-end reads for the QC pipeline. If your input file is larger, the pipeline will randomly downsample your data to 5M reads. --- [Skip to content](https://support.arimagenomics.com/migration/qc-pipeline-input-file-requirements#main-content) English Show submenu for translations ![](https://support.arimagenomics.com/hs-fs/hubfs/ArimaGenomics_Logo_White_Large_150dpi.png?width=100&height=75&name=ArimaGenomics_Logo_White_Large_150dpi.png) - [Services](https://support.arimagenomics.com/migration/qc-pipeline-input-file-requirements#services) - [Blog](https://support.arimagenomics.com/migration/qc-pipeline-input-file-requirements#blog) - [Gallery](https://support.arimagenomics.com/migration/qc-pipeline-input-file-requirements#gallery) - [About](https://support.arimagenomics.com/migration/qc-pipeline-input-file-requirements#about) Open main navigation Close main navigation - [Services](https://support.arimagenomics.com/migration/qc-pipeline-input-file-requirements#services) - [Blog](https://support.arimagenomics.com/migration/qc-pipeline-input-file-requirements#blog) - [Gallery](https://support.arimagenomics.com/migration/qc-pipeline-input-file-requirements#gallery) - [About](https://support.arimagenomics.com/migration/qc-pipeline-input-file-requirements#about) - English Show submenu for translations - Contact us Contact us How can we help you? - There are no suggestions because the search field is empty. 1. [Help Center](https://support.arimagenomics.com/migration/?hsLang=en) 2. [QC Pipeline FAQ](https://support.arimagenomics.com/migration//qc-pipeline-faq?hsLang=en) # What are the input file requirements for the QC pipeline? We recommend between 0.5 and 2M paired-end reads for the QC pipeline. If your input file is larger, the pipeline will randomly downsample your data to 5M reads. As a reminder, the FASTQ files you get from the sequencer for each sample you sequence typically contain one file of forward reads (R1) and one file of reverse reads (R2), so you will have two .fastq files per sample. - [SV Pipeline FAQ](https://support.arimagenomics.com/migration//sv-pipeline-faq?hsLang=en) - [QC Pipeline FAQ](https://support.arimagenomics.com/migration//qc-pipeline-faq?hsLang=en) - [General Portal FAQ](https://support.arimagenomics.com/migration//general-portal-faq?hsLang=en) - [Services](https://support.arimagenomics.com/migration/qc-pipeline-input-file-requirements#services) - [Blog](https://support.arimagenomics.com/migration/qc-pipeline-input-file-requirements#blog) - [Gallery](https://support.arimagenomics.com/migration/qc-pipeline-input-file-requirements#gallery) - [About](https://support.arimagenomics.com/migration/qc-pipeline-input-file-requirements#about) [![Chill listening crop-3](https://support.arimagenomics.com/hs-fs/hubfs/ArimaGenomics_Logo_FullColor_Web_600x193px.png?width=170&height=55&name=ArimaGenomics_Logo_FullColor_Web_600x193px.png "Chill listening crop-3")](http://arimagenomics.com) [mailto:email@email.com](mailto:email@email.com) Copyright © 2026, Arima Genomics