ArticleBMC bioinformatics2020
PyIR: a scalable wrapper for processing billions of immunoglobulin and T cell receptor sequences using IgBLAST.
Article in BMC bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- H3BERTa: A CDR-H3-specific language model for antibody repertoire analysis.Patterns (New York, N.Y.) · 2026Article
- Epitope-focused discovery of SARS-CoV-2 antibodies that potently neutralize Omicron variants.Nature microbiology · 2026Article
- Deep generative modeling captures maturation-dependent pairing patterns in human antibodies.iScience · 2026Article
- A protective and heterosubtypic antibody lineage targeting the influenza A virus neuraminidase active site.The Journal of clinical investigation · 2025Article
- Profiling antigen-binding affinity of B cell repertoires in tumors by deep learning predicts immune-checkpoint inhibitor treatment outcomes.Nature cancer · 2025Article
- clonevdjseq: A workflow and bioinformatics management system for sequencing, archiving, and analysis of VDJ sequences from clonal libraries.BMC bioinformatics · 2025Article
- Novel polymorphic and copy number diversity in the antibody IGH locus of South African individuals.Immunogenetics · 2024Article
- An explainable language model for antibody specificity prediction using curated influenza hemagglutinin antibodies.Immunity · 2024Article
- Isolation of human antibodies against influenza B neuraminidase and mechanisms of protection at the airway interface.Immunity · 2024Article
- Widespread impact of immunoglobulin V-gene allelic polymorphisms on antibody reactivity.Cell reports · 2023Article
- An explainable language model for antibody specificity prediction using curated influenza hemagglutinin antibodies.bioRxiv : the preprint server for biology · 2023Article
- Widespread impact of immunoglobulin V gene allelic polymorphisms on antibody reactivity.bioRxiv : the preprint server for biology · 2023Article
- Systematic analysis of human antibody response to ebolavirus glycoprotein shows high prevalence of neutralizing public clonotypes.Cell reports · 2023Article
- Article
- Human antibodies to SARS-CoV-2 with a recurring YYDRxG motif retain binding and neutralization to variants of concern including Omicron.Communications biology · 2022Article
- A large-scale systematic survey reveals recurring molecular features of public antibody responses to SARS-CoV-2.Immunity · 2022Article
- Computational identification of HCV neutralizing antibodies with a common HCDR3 disulfide bond motif in the antibody repertoires of infected individuals.Nature communications · 2022Review
- A large-scale systematic survey of SARS-CoV-2 antibodies reveals recurring molecular features.bioRxiv : the preprint server for biology · 2021Article
- Convergent antibody responses to the SARS-CoV-2 spike protein in convalescent and vaccinated individuals.Cell reports · 2021Article
- Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
backgroundRecent advances in DNA sequencing technologies have enabled significant leaps in capacity to generate large volumes of DNA sequence data, which has spurred a rapid growth in the use of bioinformatics as a means of interrogating antibody variable gene repertoires. Common tools used for annotation of antibody sequences are often limited in functionality, modularity and usability.
resultsWe have developed PyIR, a Python wrapper and library for IgBLAST, which offers a minimal setup CLI and API, FASTQ support, file chunking for large sequence files, JSON and Python dictionary output, and built-in sequence filtering.
conclusionsPyIR offers improved processing speed over multithreaded IgBLAST (version 1.14) when spawning more than 16 processes on a single computer system. Its customizable filtering and data encapsulation allow it to be adapted to a wide range of computing environments. The API allows for IgBLAST to be used in customized bioinformatics workflows.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.