{"repo":"nf-core/airrflow","free":true,"listed":false,"github":"https://github.com/nf-core/airrflow","clone":"git clone https://github.com/nf-core/airrflow.git","description":"B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework","language":"Nextflow","stars":78,"topics":["b-cell","immcantation","immunorepertoire","repseq","nf-core","nextflow","workflow","pipeline","airr"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/airrflow is a bioinformatics best-practice pipeline to analyze B-cell receptor (BCR) or T-cell receptor (TCR) repertoire sequencing data. It allows the processing of targeted bulk and single-cell adaptive immune receptor sequencing data (AIRR-seq), as well as the extraction of TCR and BCR sequences from untargeted bulk and single-cell RNA-seq data. The pipeline enables an end-to-end analysis, departing from raw reads or assembled sequences, and performs sequence assembly, V(D)J assignment, novel allele identification, genotype inference, clonal inference, repertoire analysis, lineage reconstruction and BCR/TCR sequence embedding using the Immcantation framework, as well as other immune repertoire analysis tools. The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from nf-core/modules in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community! On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has se","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/airrflow/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}