MiAIRR-to-NCBI Implementation

Authors:

Christian E. Busse, Florian Rubelt and Syed Ahmad Chan Bukhari

Table of Contents

• Guide for submission of AIRR-seq data to NCBI
• MiAIRR-to-NCBI Submission Manual
  • Scope of this document
  • Step 1. MiAIRR data submission to BioProject, BioSample and SRA
  • Step 2. Processed MiAIRR data submission to GenBank/TLS
• MiAIRR-to-NCBI Specification
  • Outline of INSDC reporting procedure
  • Element mapping
  • References
  • Footnotes
  • Appendix

Introduction

The MiAIRR standard

The MiAIRR standard (minimal information about adaptive immune receptor repertoires) is a minimal reporting standard for experiments using sequencing-based technologies to study adaptive immune receptors (e.g. T cell receptors or immunoglobulins). It is developed and maintained by the Minimal Standards Working Group of the Adaptive Immune Receptors Repertoire (AIRR) Community [Breden_2017]. The current version (1.0) of the standard has been recently published [Rubelt_2017] and was passed by the general assembly at the annual AIRR Community meeting in December 2017. MiAIRR requires researchers to report six sets of information:

1. study, subject, diagnosis & intervention

2. sample collection

3. sample processing and sequencing

4. raw sequencing data

5. data processing

6. processed sequences with a basic analysis results

However, MiAIRR only describes the mandatory data items that have to be reported, but neither provides details how and where to deposit data nor specifies data types and formats. Therefore this document aims to provide both a submission manual for users as well as a detailed data specification for developers.