scifer

scifer integrates Sanger sequencing data with flow cytometry index sort data for quality control and analysis of immune receptor sequences from single-cell sorted B cells and T cells.

Key Features:

• Quality Control of Sanger Sequences: Identifies high-quality sequences based on length, Phred scores, and heavy-chain complementarity-determining region 3 (HCDR3) quality.
• Flow Cytometry Integration: Merges flow cytometry data from probed single-cell sorted B cells with sequencing data to identify which cell was sorted where.
• Electropherogram Generation: Produces electropherograms for visual inspection of sequence quality.
• Export Capabilities: Exports summary tables, FASTA files, and quality control reports.
• Large-Scale Processing: Automates processing of thousands of sequences in less than an hour.
• Germline Assignment Improvement: Significantly increases quality of germline assignments and reduces spurious variable gene mutations.

Scientific Applications:

• B Cell Receptor Analysis: Processes and analyzes B cell receptor sequences from index-sorted single cells probed with flow cytometry.
• T Cell Receptor Analysis: Processes and analyzes T cell receptor sequences from index-sorted single cells.
• Immune Repertoire Sequencing: Speeds up analysis of immune receptor repertoire sequences with wide applicability in immunological research.

Methodology:

scifer preprocesses raw data from index sorts and immune receptor Sanger sequencing, then identifies high-quality sequences based on selected parameters including length, Phred scores, and HCDR3 quality.