VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data.

ABSTRACT:

Background

Pre-processing of high-throughput sequencing data for immune repertoire profiling is essential to insure high quality input for downstream analysis. VDJPipe is a flexible, high-performance tool that can perform multiple pre-processing tasks with just a single pass over the data files.

Results

Processing tasks provided by VDJPipe include base composition statistics 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. VDJPipe utilizes a pipeline approach whereby multiple processing steps are performed in a sequential workflow, with the output of each step passed as input to the next step a

SUBMITTER: Christley S 

PROVIDER: S-EPMC5637252 | biostudies-literature | 2017 Oct

REPOSITORIES: biostudies-literature