🧬 2. Read Alignment, Spliced Mapping & Utilities

SIMD hardware-accelerated rewrite of BWA-MEM. Employs 8-way and 16-way vectorization to align short DNA reads 2x faster to human reference genomes (GRCh38/T2T).

Fast pairwise aligner for PacBio HiFi, Oxford Nanopore, spliced direct RNA, and full-genome assembly synteny. Industry standard for third-generation sequencing.

Ultrafast universal spliced RNA-seq aligner based on sequential Maximum Mappable Prefix matching. High sensitivity for non-canonical splice junctions and chimeric gene fusions.

Memory-efficient Burrows-Wheeler transform tool for aligning sequencing reads to long reference genomes. Ideal for ChIP-seq, ATAC-seq, and bacterial assemblies.

Hierarchical Graph FM index aligner capable of mapping RNA-seq reads across population-scale variant graphs, reducing reference allele alignment bias.

Ultra-fast transcript abundance quantification from RNA-seq reads using quasi-mapping with GC-bias, sequence-specific bias, and fragment-length correction.

Near-instantaneous pseudoalignment algorithm for quantifying transcript abundances from RNA-Seq reads by matching k-mers to colored de Bruijn graph paths without base-to-base alignment.

Haplotype-aware pangenome read aligner. Maps sequencing reads to variation graphs as fast as linear aligners, eliminating reference bias and uncovering structural alleles.

The essential foundational software library and command-line utilities for reading, writing, sorting, indexing, viewing, and calculating depth coverage across SAM, BAM, and CRAM alignment files.

High-performance interactive visualization tool for exploring diverse large-scale genomic datasets (BAM pileups, VCF mutations, BigWig ChIP peaks, gene annotations) in smooth real time.