Panaln: indexing pangenome for read alignment.

ABSTRACT:

Motivation

Pangenome indexing is a critical supporting technology in biological sequence analysis such as read alignment applications. The need to accurately identify billions of small sequencing fragments carrying sequencing errors and genomic variants drives the development of scalable and efficient pangenome indexing approach.

Results

We propose a new wavelet tree-based approach, called Panaln, for indexing pangenome and introduce a batch computation approach for fast count query over Panaln. We present a simple and effective seeding strategy and develop a pangenome program that uses the seed-and-extend paradigm for read alignment. Experimental results on simulated and real data demonstrate that Panaln uses significantly less space for the compared pangenome methods with

SUBMITTER: Guo L 

PROVIDER: S-EPMC12448906 | biostudies-literature | 2025 Sep

REPOSITORIES: biostudies-literature