RopeBWT2

RopeBWT2 constructs the FM-index for DNA sequences to support sequence alignment and genome analysis.

Key Features:

• Incremental Construction: Builds the FM-index by inserting one or multiple DNA sequences into an existing pseudo-BWT position-by-position starting from the end of each sequence.
• Reverse Lexicographical Sorting: Implicitly sorts sequences in reverse lexicographical order without a separate sorting step.
• Performance Efficiency: Provides high indexing performance for short DNA reads and is practical for indexing long reads averaging kilobases and genome-sized sequences.

Scientific Applications:

• Genome Analysis: Enables construction of FM-indexes for large and complex genomes to support sequence alignment and variant calling.
• Short and Long Read Sequencing: Indexes both short reads and long reads (kilobase-scale) from diverse sequencing technologies for downstream genomic analyses.

Methodology:

Incremental insertion of sequences into the pseudo-BWT position-by-position from sequence ends, combined with implicit reverse lexicographical ordering to avoid a separate sorting step.