The adaptive immune system includes populations of B and T cells capable of binding foreign epitopes via antigen specific receptors, called immunoglobulin (IG) for B cells and the T cell receptor (TCR) for T cells. In order to provide protection from a wide range of pathogens, these cells display highly diverse repertoires of IGs and TCRs. This is achieved through combinatorial rearrangement of multiple gene segments in addition, for B cells, to somatic hypermutation. Deep sequencing technologies have revolutionized analysis of the diversity of these repertoires; however, accurate TCR/IG diversity profiling requires specialist bioinformatics tools. Here we present LymAnalzyer, a software package that significantly improves the completeness and accuracy of TCR/ IG profiling from deep sequence data and includes procedures to identify novel alleles of gene segments. On real and simulated data sets LymAnalyzer produces highly accurate and complete results. Although, to date we have applied it to TCR/ IG data from human and mouse, it can be applied to data from any species for which an appropriate database of reference genes is available. Implemented in Java, it includes both a command line version and a graphical user interface and is freely available at https://sourceforge.net/projects/lymanalyzer/.