.. _CAIRR_Pipeline: ============== CAIRR Pipeline ============== Introduction: The CAIRR pipeline for submitting standards-compliant B and T cell receptor repertoire sequencing studies to the NCBI ----------------------------------------------------------------------------------------------------------------------------------- AIRR sequencing (AIRR-seq) has tremendous potential to understand the dynamics of the immune repertoire in vaccinology, infectious disease, autoimmunity, and cancer biology. The adaptation of high-throughput sequencing (HTS) for AIRR (Adaptive Immune Receptor Repertoire) studies has made possible to characterize the AIRR at unprecedented depth and the outcome of such sequencing produces big data. Effective sharing of AIRR-seq big data could potentially reveal amazing scientific insights. The AIRR Community has proposed MiAIRR (Minimum information about an Adaptive Immune Receptor Repertoire Sequencing Experiment), a standard for reporting AIRR-seq studies. The MiAIRR standard has been implemented using the National Center for Biotechnology Information (NCBI) repositories. Submissions of AIRR-seq data to the NCBI repositories typically use a combination of web-based and flat-file templates and include only a minimal amount of terminology validation. As a result, AIRR-seq studies at the NCBI are often described using inconsistent terminologies, limiting scientists' ability to access, find, interoperate, and reuse the data sets and to understand how the experiments were performed. CEDAR (Center for Expanded Data Annotation and Retrieval) develops technologies involving the use of data standards and ontologies to improve metadata quality. In order to improve metadata quality and ease AIRR-seq study submission process, we have developed an AIRR-seq data submission pipeline named CEDAR-AIRR (CAIRR). CAIRR leverages CEDAR's technologies to: i) create web-based templates whose entries are controlled by ontology terms, ii) generate and validate metadata and iii) submit the ontology-linked metadata and sequence files (FASTQ) to the NCBI BioProject, BioSample, and Sequence Read Archive (SRA) databases. Thus, CAIRR provides a web-based metadata submission interface that supports compliance with MiAIRR standards. The interface enables ontology-based validation for several data elements, including: organism, disease, cell type and subtype, and tissue. This pipeline will facilitate the NCBI submission process and improve the metadata quality of AIRR-seq studies. Submission Steps ---------------- The submission steps are described in the MiAIRR-to-NCBI Submission Manual: :ref:`MiAIRR_NCBI_Submission_Manual_Option_1`. You will need a CEDAR system account; you can self-register at https://cedar.metadatacenter.org. You will also need the identifier of a BioProject already entered in the NCBI BioProject database. Citing the MiAIRR Pipeline -------------------------- Bukhari, Syed Ahmad Chan, Martin J. O'Connor, Marcos Martínez-Romero, Attila L. Egyedi, Debra Debra Willrett, John Graybeal, Mark A. Musen, Florian Rubelt, Kei H. Cheung, and Steven H. Kleinstein. `The CAIRR pipeline for submitting standards-compliant B and T cell receptor repertoire sequencing studies to the NCBI `_. Frontiers in Immunology 9 (2018): 1877. DOI: 10.3389/fimmu.2018.01877 Tell Us About It ---------------- Please let us know how it went! If you are willing, we would love to have your comments in a `short survey `_, it should just take 5 minutes or so. We also welcome entry of issues and requests in our `github repository issues `_, and emails can be sent to cedar-users@lists.stanford.edu. Both of these resources are publicly visible. Support or Contact ------------------ Having trouble with NCBI submission process through our pipeline? Please email to `Syed Ahmad Chan Bukhari `_ or to `Marcos Martínez-Romero `_ and we will help you sort it out.