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Fig. 1 | BMC Bioinformatics

Fig. 1

From: TRIg: a robust alignment pipeline for non-regular T-cell receptor and immunoglobulin sequences

Fig. 1

TRIg pipeline. TRIg starts by aligning TR or Ig reads to the corresponding reference using nucmer. Because many initial alignments overlap, thus not authentic, optimal sets of alignments are obtained using a heuristic iterative approach. Some of the optimal alignments are further filtered based on the VDJ annotations. If more than one V annotation survives the filtering, TRIg intends to extend the alignments by relaxing the breaklen parameter of nucmer, followed by re-identification of authentic alignments. Because the resulting alignments may still overlap by few bases, the overlapping bases are trimmed (in red). Finally, VDJ annotations are collected and the CDR3 segments are extracted. Please see main text for detailed descriptions

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