Scifer: An R/Bioconductor package for large-scale integration of Sanger sequencing and flow cytometry data of index-sorted single cells

Here you will find all the data, code, and analysis used for the scifer manuscript. scifer is an R/Bioconductor package that can preprocess raw data from index sorts and raw BCR Sanger sequencing data. It can identify high-quality sequences based on different parameters, such as length, Phred scores, and heavy-chain complementarity-determining region 3 (HCDR3) quality. As a result, it significantly increases the quality of germline assignments and reduces spurious variable gene mutations. Its output provides quality control reports, FASTA files, summarized tables, and electropherograms for manual inspection.