pRESTO

pRESTO processes raw high-throughput sequencing reads of lymphocyte repertoires to produce error-corrected, sorted, and annotated sequence sets for characterization of B-cell immunoglobulin repertoires and their germline and somatic diversity.

Key Features:

• Platform-independent Python modules: Implemented as platform-independent Python modules for processing raw reads from high-throughput sequencing of lymphocyte repertoires.
• Error correction and annotation: Processes raw sequencing data into error-corrected, sorted, and annotated sequence sets suitable for downstream repertoire analysis.
• Comprehensive metrics generation: Produces detailed metrics at each processing step to support quality control and data characterization.
• Sequencing technology support: Handles multiplexed primer pools, single- or paired-end sequencing, and workflows incorporating single-molecule identifiers.
• Platform testing: Tested on data from Roche and Illumina sequencing platforms.
• Parallel processing: Supports parallelization of computational steps across available processors to improve throughput on large datasets.

Scientific Applications:

• Lymphocyte repertoire sequencing: Supports high-throughput sequencing studies of lymphocyte receptor repertoires, including B-cell immunoglobulins.
• Immune diversity analysis: Enables analysis of immune diversity through high-quality annotated sequences and stepwise QC metrics.
• Clonal composition and evolution: Enables analyses of clonal composition and somatic evolution within repertoires.
• Response monitoring: Enables analysis of responses to infection or vaccination.
• Disease mechanism investigation: Enables study of immune-associated disease mechanisms.

Methodology:

Implemented as platform-independent Python modules that process raw high-throughput sequencing reads into error-corrected, sorted, and annotated sequences, generate detailed per-step metrics, support multiplexed primer pools, single- or paired-end reads and single-molecule identifiers, and parallelize computational steps across available processors.