Trigs is an expanding set of tools for downstream analysis of Ig repertoire sets. All tools are available for download from GitHub.
AnnotateTree creates annotated lineage trees and sequence alignments showing the point at which amino acid substitutions occur. It uses PHYLIP’s dnaml for ancestral reconstruction. Sequence numbering can be defined by the user, for example to match the numbering of a crystal structure, or to match a standard numbering scheme. If the sequences represent a B-cell clonal lineage, additional reports relating to variation in the CDRs can be produced.
RevertToGermline uses a simple approach to infer the germline ancestor of a B-cell variable region sequence, given the IMGT junction analysis. If a clonal lineage is available, the inferred germline can be used to root a phylogenetic tree, from which a more accurate germline can then be inferred using AnnotateTree.
Clustering tools support the clustering of sequences for clonal analysis, and their large-scale depiction.
Tools for junction parsing and results manipluation support the integration of IgBLAST into an IMGT-style pipeline, and ease the processing of tab-separated analysis files.
FASTA tools support small NGS-oriented operations on FASTA files.
This document describes the use of Trigs in a recent analysis.
July 2016 - Significant update, including clustering and germline analysis tools.
October 2015 - Added Tools for processing IgBLAST analysis files and for extracting sequences from IMGT/IGBLAST reports.
September 2015 - AnnotateTree now generates a frequency-based logo plot, showing the occurrence of amino acids in the input sequence set. This optional facility requires installation of Berkeley Weblogo (see the documentation for details).
The tools and website are described in the following article: please reference it you use them in your research.
William D. Lees and Adrian J. Shepherd, “Utilities for High-Throughput Analysis of B-Cell Clonal Lineages,” Journal of Immunology Research, vol. 2015, Article ID 323506, 9 pages, 2015. doi:10.1155/2015/323506