Tangram

Tangram detects mobile element insertions (MEIs) from short-read next-generation sequencing alignments to identify ALU, long interspersed nuclear elements (LINE-1), and SVA insertions that contribute to genomic variability and disease-associated events.

Key Features:

• MEI detection: Detects mobile element insertions including ALU, long interspersed nuclear elements (LINE-1), and SVA elements.
• Input data: Operates on short-read next-generation sequencing alignments.
• Mapper compatibility: Leverages mapping information from the MOSAIK mapper and supports alignments produced by any mainstream short-read mapper.
• Development history: Originally depended on MOSAIK alignments and was enhanced to accept alignments from other mainstream short-read mappers.
• Performance: Demonstrates accuracy and speed suitable for large-scale genomic datasets.
• Validation datasets: Has been applied to datasets from the 1000 Genomes Project and The Cancer Genome Atlas (TCGA) mutation calling benchmark 4.

Scientific Applications:

• 1000 Genomes Project: Used as a primary MEI detection tool in the 1000 Genomes Project analyses.
• TCGA mutation calling benchmark 4: Applied to TCGA benchmark 4 datasets for cancer genome analysis.
• Cancer genome analysis: Supports identification of MEIs relevant to cancer-associated genomic events.
• Genomic variability and evolution: Characterizes contributions of mobile elements to human genomic diversity and evolution.

Methodology:

Analyzes alignment mapping information—originally MOSAIK-specific and now compatible with mainstream short-read mappers—to detect MEIs (ALU, LINE-1, SVA) in short-read NGS data.