--- title: Requirements for submitted FASTQ files description: "The accepted input files to run analyses on VarSome Clinical are either: Paired-end reads must be provided in two different files, e.g.: sample_R1.fastq.gz and sample_R2.fastq.gz. We expect files that" --- [Skip to content](https://docs.varsome.com/en/accepted-input-files#main-content) English Show submenu for translations [Submit a Support Request](https://docs.varsome.com/en/kb-tickets/new?hsLang=en) [Customer portal](https://docs.varsome.com/support-requests?hsLang=en) [![varsome-new.png\]](https://docs.varsome.com/hs-fs/hubfs/varsome-new.png?height=40&name=varsome-new.png)](https://docs.varsome.com/en?hsLang=en) - Editions Show submenu for Editions - [VarSome.com](https://landing.varsome.com/varsome) - [VarSome Clinical](https://landing.varsome.com/varsome-clinical) - [VarSome Premium](https://landing.varsome.com/varsome-premium) - [VarSome API](https://landing.varsome.com/varsome-api) - [VarSome Insights](https://landing.varsome.com/varsome-insights) - About Show submenu for About - [The Company](https://saphetor.com/) - [Contact Us](https://landing.varsome.com/contact) - [Distributors](https://landing.varsome.com/distributors) - [Become a Partner](https://landing.varsome.com/become-varsome-partner) - [Community](https://varsome.com/community-contributions/) - [Cite VarSome!](https://varsome.com/about/general/varsome-citations/) - Resources Show submenu for Resources - [Datasources](https://varsome.com/datasources/) - [Germline Classification](https://varsome.com/about/resources/germline-implementation/) - [Somatic Classification](https://varsome.com/about/resources/somatic-implementation/) - [CNV Classification](https://varsome.com/about/resources/sv-implementation/) - [Help Center](https://docs.varsome.com/) - [Library](https://landing.varsome.com/whitepapers) - [IVDR](https://landing.varsome.com/ivdr-whitepaper) - [Legal & Compliance](https://docs.varsome.com/en/legal-compliance) - Blog Show submenu for Blog - [Platform Updates](https://updates.varsome.com/en) - [Company News](https://news.varsome.com/en) - [VarSome Annotated](https://blog.varsome.com/annotated) Open main navigation Close main navigation - Editions Show submenu for Editions - [VarSome.com](https://landing.varsome.com/varsome) - [VarSome Clinical](https://landing.varsome.com/varsome-clinical) - [VarSome Premium](https://landing.varsome.com/varsome-premium) - [VarSome API](https://landing.varsome.com/varsome-api) - [VarSome Insights](https://landing.varsome.com/varsome-insights) - About Show submenu for About - [The Company](https://saphetor.com/) - [Contact Us](https://landing.varsome.com/contact) - [Distributors](https://landing.varsome.com/distributors) - [Become a Partner](https://landing.varsome.com/become-varsome-partner) - [Community](https://varsome.com/community-contributions/) - [Cite VarSome!](https://varsome.com/about/general/varsome-citations/) - Resources Show submenu for Resources - [Datasources](https://varsome.com/datasources/) - [Germline Classification](https://varsome.com/about/resources/germline-implementation/) - [Somatic Classification](https://varsome.com/about/resources/somatic-implementation/) - [CNV Classification](https://varsome.com/about/resources/sv-implementation/) - [Help Center](https://docs.varsome.com/) - [Library](https://landing.varsome.com/whitepapers) - [IVDR](https://landing.varsome.com/ivdr-whitepaper) - [Legal & Compliance](https://docs.varsome.com/en/legal-compliance) - Blog Show submenu for Blog - [Platform Updates](https://updates.varsome.com/en) - [Company News](https://news.varsome.com/en) - [VarSome Annotated](https://blog.varsome.com/annotated) - English Show submenu for translations - [Submit a Support Request](https://docs.varsome.com/en/kb-tickets/new) - [Customer portal](https://docs.varsome.com/support-requests) - [Contact us](https://docs.varsome.com/en/kb-tickets/new) [Contact us](https://docs.varsome.com/en/kb-tickets/new?hsLang=en) How can we help you? - There are no suggestions because the search field is empty. 1. [VarSome Help Center](https://docs.varsome.com/en?hsLang=en) 2. [Management of Samples and Analyses](https://docs.varsome.com/en/management-of-samples-and-analyses?hsLang=en) 3. [Uploading files](https://docs.varsome.com/en/management-of-samples-and-analyses?hsLang=en#uploading-files) # Requirements for submitted FASTQ files [VarSome Clinical](https://saphetor.com/varsome-editions/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](https://support.illumina.com/help/BaseSpace_OLH_009008/Content/Source/Informatics/BS/NamingConvention_FASTQ-files-swBS.htm.).    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](https://en.mgi-tech.com/contact/).  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 - [Registration & Billing](https://docs.varsome.com/en/registration-billing?hsLang=en#main-content) - [User account management](https://docs.varsome.com/en/registration-billing?hsLang=en#user-account-management) - [Storage management](https://docs.varsome.com/en/registration-billing?hsLang=en#storage-management) - [Pricing and Billing](https://docs.varsome.com/en/registration-billing?hsLang=en#pricing-and-billing) - [VarSome Clinical Tokens](https://docs.varsome.com/en/registration-billing?hsLang=en#varsome-clinical-tokens) - [Management of Samples and Analyses](https://docs.varsome.com/en/management-of-samples-and-analyses?hsLang=en#main-content) - [Uploading files](https://docs.varsome.com/en/management-of-samples-and-analyses?hsLang=en#uploading-files) - [Managing Samples](https://docs.varsome.com/en/management-of-samples-and-analyses?hsLang=en#managing-samples) - [Managing Workflows](https://docs.varsome.com/en/management-of-samples-and-analyses?hsLang=en#managing-workflows) - [Launching analyses](https://docs.varsome.com/en/management-of-samples-and-analyses?hsLang=en#launching-analyses) - [Analysis of the results](https://docs.varsome.com/en/analysis-of-the-results?hsLang=en#main-content) - [Analyses](https://docs.varsome.com/en/analysis-of-the-results?hsLang=en#analyses) - [Results](https://docs.varsome.com/en/analysis-of-the-results?hsLang=en#results) - [Filters](https://docs.varsome.com/en/analysis-of-the-results?hsLang=en#filters) - [Reporting](https://docs.varsome.com/en/analysis-of-the-results?hsLang=en#reporting) - [Quality Control](https://docs.varsome.com/en/analysis-of-the-results?hsLang=en#quality-control) - [Legal & compliance](https://docs.varsome.com/en/legal-compliance?hsLang=en) - [FAQ & Troubleshooting](https://docs.varsome.com/en/faq-troubleshooting?hsLang=en#main-content) - [Troubleshooting](https://docs.varsome.com/en/faq-troubleshooting?hsLang=en#troubleshooting) - [General](https://docs.varsome.com/en/faq-troubleshooting?hsLang=en#general) - [Filters](https://docs.varsome.com/en/faq-troubleshooting?hsLang=en#filters) - [User Interface](https://docs.varsome.com/en/faq-troubleshooting?hsLang=en#user-interface) - [Pipelines](https://docs.varsome.com/en/faq-troubleshooting?hsLang=en#pipelines) - [Features](https://docs.varsome.com/en/faq-troubleshooting?hsLang=en#features) - [Scientific articles](https://docs.varsome.com/en/scientific-articles?hsLang=en) - [VarSome API](https://docs.varsome.com/en/varsome-api?hsLang=en) [![VarSome Logo](https://docs.varsome.com/hs-fs/hubfs/VarSome%20Logo.png?width=200&height=47&name=VarSome%20Logo.png "VarSome Logo")](https://varsome.com) **Resources** [Query Examples](https://varsome.com/about/resources/examples/) [Germline Classification](https://varsome.com/about/resources/germline-implementation/) [Somatic Classification](https://varsome.com/about/resources/somatic-implementation/) [White Papers & Other Resources](https://varsome.com/library/) [Cite VarSome](https://varsome.com/about/general/varsome-citations/) [System Status](https://status.saphetor.com/) [Help Center](https://docs.varsome.com/en?hsLang=en) **Legal** [Terms of Use](https://varsome.com/information/legal/terms/) [Privacy Policy](https://varsome.com/information/legal/privacy/) [Information Security](https://varsome.com/information/legal/information-security/) Copyright © 2025, Saphetor SA