Rapid and accurate alignment of nucleotide conversion sequencing reads with HISAT-3N

Sequencing technologies using nucleotide conversion techniques such as cytosine to thymine in bisulfite-seq and thymine to cytosine in SLAM seq are powerful tools to explore the chemical intricacies of cellular processes. To date, no one has developed a unified methodology for aligning converted seq...

Full description

Saved in:
Bibliographic Details
Published in:Genome research 2021-07, Vol.31 (7), p.1290-1295
Main Authors: Zhang, Yun, Park, Chanhee, Bennett, Christopher, Thornton, Micah, Kim, Daehwan
Format: Article
Language:English
Subjects:
Bisulfite
Cytosine
Method
Thymine
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Sequencing technologies using nucleotide conversion techniques such as cytosine to thymine in bisulfite-seq and thymine to cytosine in SLAM seq are powerful tools to explore the chemical intricacies of cellular processes. To date, no one has developed a unified methodology for aligning converted sequences and consolidating alignment of these technologies in one package. In this paper, we describe hierarchical indexing for spliced alignment of transcripts-3 nucleotides (HISAT-3N), which can rapidly and accurately align sequences consisting of any nucleotide conversion by leveraging the powerful hierarchical index and repeat index algorithms originally developed for the HISAT software. Tests on real and simulated data sets show that HISAT-3N is faster than other modern systems, with greater alignment accuracy, higher scalability, and smaller memory requirements. HISAT-3N therefore becomes an ideal aligner when used with converted sequence technologies.
ISSN:1088-9051
1549-5469
DOI:10.1101/gr.275193.120