graphmap

graphmap aligns long, error-prone nanopore and Pacific Biosciences (PacBio) sequencing reads to reference genomes to enable accurate read alignment, single-nucleotide variant calling, structural variant detection, and pathogen/strain identification.

Key Features:

• Long-read support: Handles nanopore (including MinION and Oxford Nanopore) and Pacific Biosciences (PacBio) long reads and is robust to high sequencing error rates.
• Graph-based mapping algorithm: Employs a graph-based mapping algorithm that progressively refines candidate alignments and uses fast graph traversal.
• Alignment accuracy: Reports alignment accuracy greater than 95%.
• Increased mapping sensitivity: Enhances mapping sensitivity by 10–80% relative to existing short- and long-read mappers.
• High base mapping rate: Successfully maps over 95% of bases.
• Single-nucleotide variant support: Enables SNV calling on the human genome with a reported ~15% increase in sensitivity versus the next best mapper.
• Structural variant detection: Detects structural variants in the range of 100 bp to 4 kbp.
• Pathogen/strain identification: Supports species- and strain-specific identification of pathogens using MinION reads.
• Graphmap2 splice-aware RNA mapping: Extends mapping to splice-aware alignment of long RNA reads from Pacific Biosciences and Oxford Nanopore devices.
• Transcript and exon detection: Graphmap2 algorithms report higher precision and recall in detecting transcripts and exon boundaries and improved mappability compared with Minimap2 and Gmap on reported datasets.
• Isoform and gene discovery: Facilitates discovery of previously unknown isoforms and genes from long-read RNA-seq data.

Scientific Applications:

• Long-read genome alignment: Aligns nanopore and PacBio reads for downstream genomic analyses.
• Variant discovery: Supports single-nucleotide variant calling and improves sensitivity for human-genome SNV detection.
• Structural variant analysis: Detects structural variants from 100 bp to 4 kbp using long-read alignments.
• Pathogen identification and strain typing: Enables species- and strain-level identification from MinION sequencing data.
• Transcriptomics and isoform discovery: Performs splice-aware mapping of long RNA reads to detect transcripts, exon boundaries, and novel isoforms/genes.

Methodology:

Uses a graph-based mapping algorithm that progressively refines candidate alignments via fast graph traversal; Graphmap2 adds splice-aware mapping algorithms for long RNA reads to improve transcript and exon boundary detection.