Introduction

pRESTO is a toolkit for processing raw reads from high-throughput sequencing of lymphocyte repertoires.

Dramatic improvements in high-throughput sequencing technologies now enable large-scale characterization of immunoglobulin repertoires, defined as the collection of trans-membrane antigen-receptor proteins located on the surface of T and B lymphocytes. The REpertoire Sequencing TOolkit (pRESTO) is composed of a suite of utilities to handle all stages of sequence processing prior to germline segment assignment. pRESTO is designed to handle either single reads or paired-end reads. It includes features for quality control, primer masking, annotation of reads with sequence embedded barcodes, generation of single-molecule consensus sequences, assembly of paired-end reads and identification of duplicate sequences. Numerous options for sequence sorting, sampling and conversion operations are also included.

pRESTO Tools

• AlignSets
  Provides operations to multiple align sets of sequences sharing the same annotation.
• AssemblePairs
  Assembles paired-end reads into a complete sequence.
• BuildConsensus
  Constructs a consensus sequence from sets of sequences sharing the same annotation.
• ClusterSets
  Clusters groups of sequences sharing an annotation into sub-clusters.
• CollapseSeq
  Removes duplicate sequences.
• ConvertHeaders
  Converts sequence headers into the pRESTO annotation format.
• EstimateError
  Generates an estimate of the sequencing error rates for a data set using UID read group information.
• FilterSeq
  Filters sequences to high-quality reads using a variety of criteria.
• MaskPrimers
  Trims or masks primer and barcode sequences in multiplexed runs and annotates reads accordingly.
• PairSeq
  Uniformly sorts paired-end read files and copies annotations between mate-pairs.
• ParseHeaders
  Manipulates sequence annotations.
• ParseLog
  Converts the log output of pRESTO scripts into data tables.
• SplitSeq
  Performs sampling, sorting and subsetting of sequence files.

Citation

pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires
Vander Heiden JA*, Yaari G*, Uduman M, Stern JNH, O'Connor KC, Hafler DA, Vigneault F, Kleinstein SH
Bioinformatics 2014; doi: 10.1093/bioinformatics/btu138

Additional Ig Repertoire Tools

• BASELINe
  Bayesian estimation of antigen-driven selection.
  
• Change-O
  Clonal assignment, lineage reconstruction, diversity analysis, mutation profiling and selection analysis.
  
• TIgGER
  Personal genotyping assignment and novel polymorphism detection.
  
• S5F
  A 5-mer microsequence context model of somatic hypermutation targeting and substitution rates.