Graphmap2

Graphmap2 maps long, error-prone RNA sequencing reads from Pacific Biosciences and Oxford Nanopore platforms to reference genomes with splice awareness to identify exon boundaries and transcript isoforms.

Key Features:

• Splice-Aware Mapping: Recognizes and accurately maps RNA transcripts and their exon boundaries from long-read RNA-seq data.
• Algorithmic Innovations: Implements newly developed algorithms that improve precision and recall in detecting mapped transcripts and exon ends, reporting superior performance relative to Minimap2 and Gmap.
• High Mappability: Demonstrates increased mappability rates on simulated and real datasets, yielding more aligned reads to the reference genome.
• Exon Boundary Detection: Detects exon boundaries with increased accuracy to support detailed transcriptome analysis and isoform identification.

Scientific Applications:

• Identification of Novel Isoforms: Enables discovery of previously unannotated transcript isoforms through precise exon boundary detection.
• Gene Discovery: Facilitates identification of novel genes, aiding studies of genomic complexity and evolution.
• Transcriptome Analysis: Supports comprehensive transcriptome studies using long-read RNA-seq data from Pacific Biosciences and Oxford Nanopore platforms.

Methodology:

Builds upon the foundational algorithms of Graphmap and applies alignment techniques that model splicing events and tolerate sequencing errors typical of long-read technologies.