tophat2

tophat2 aligns RNA-sequence (RNA-seq) reads to a reference genome to identify spliced alignments, novel splice junctions, variable-length insertions and deletions, and fusion breakpoints from next-generation sequencing data.

Key Features:

• Variable-Length Indels: Aligns reads containing variable-length insertions and deletions relative to a reference genome to accommodate diverse read lengths from next-generation sequencing.
• De Novo Spliced Alignment: Identifies novel splice sites and spliced alignments without relying on pre-existing gene annotations.
• Alignment Across Fusion Breaks: Aligns reads spanning fusion breakpoints arising from genomic translocations to support detection of fusion events.
• Sensitivity and Accuracy: Combines novel splice site identification with direct mapping to known transcripts to improve sensitivity and accuracy in challenging contexts such as highly repetitive genomes and pseudogenes.
• High Throughput: Optimized for high-throughput mapping, capable of processing millions of reads per CPU hour.

Scientific Applications:

• Alternative Splicing and Transcript Discovery: Detection of novel splice junctions and discovery of new transcripts in transcriptome studies.
• Gene Expression Regulation Studies: Mapping RNA-seq reads for analyses of gene expression and regulatory events.
• Cancer Genomics: Detection and characterization of fusion events and chromosomal rearrangements resulting from genomic translocations.
• Analysis of Repetitive Genomes: Accurate alignment in genomes with high repetitiveness or abundant pseudogenes to aid transcriptome characterization.

Methodology:

tophat2 employs an advanced read-mapping algorithm that does not depend on known splice junctions, enabling ab initio splice site discovery and combining novel splice site identification with direct mapping to known transcripts.