TY  - JOUR
A1  - Zhang, Yun
A1  - Park, Chanhee
A1  - Bennett, Christopher
A1  - Thornton, Micah
A1  - Kim, Daehwan
T1  - Rapid and accurate alignment of nucleotide conversion sequencing reads with HISAT-3N
Y1  - 2021/06/08 
JF  - Genome Research 
JO  - Genome Research 
DO  - 10.1101/gr.275193.120 
SP  - gr.275193.120 
UR  - http://genome.cshlp.org/content/early/2021/06/08/gr.275193.120.abstract 
N2  - Sequencing technologies utilizing 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 HISAT-3N (hierarchical indexing for spliced alignment of transcripts - 3 nucleotides), 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 demonstrate 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. 
ER  -