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

Yun Zhang, Chanhee Park, Christopher Bennett, Micah Thornton, Daehwan Kim

Research output: Contribution to journalArticlepeer-review

34 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)1290-1295
Number of pages6
JournalGenome Research
Issue number7
StatePublished - Jul 2021

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)


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