RT Journal
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
JF Genome Research 
JO Genome Research 
YR 2021 
FD July 01 
VO 31 
IS 7 
SP 1290 
OP 1295 
DO 10.1101/gr.275193.120 
UL http://genome.cshlp.org/content/31/7/1290.abstract 
AB 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.