VDJPipe is a tool to pre-process immune repertoire sequencing data. The VDJPipe package includes functions for base composition statistics the calculation, read quality statistics calculation, quality filtering, homopolymer filtering, length, and nucleotide filtering, paired-read merging, barcode demultiplexing, 5' and 3' PCR primer matching, and duplicate reads collapsing.
RNA-seq
Christley S, Levin MK, Toby IT, Fonner JM, Monson NL, Rounds WH, Rubelt F, Scarborough W, Scheuermann RH, Cowell LG "VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data." BMC Bioinformatics. 2017 Oct 11;18(1):448. https://doi.org/10.1186/s12859-017-1853-z
PMID: 29020925
PMCID: PMC5637252
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