PyIR: a scalable wrapper for processing billions of immunoglobulin and T cell receptor sequences using IgBLAST
2020
Cinque Soto | Jessica A. Finn | Jordan R. Willis | Samuel B. Day | Robert S. Sinkovits | Taylor Jones | Samuel Schmitz | Jens Meiler | Andre Branchizio | James E. Crowe
Abstract Background Recent 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. Results We 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. Conclusions PyIR 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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