Short-tandem repeats (STRs) are type of genetic markers distinguishing individuals and authenticating cell-lines. Nanopore sequencing is promising in STR typing for its convenience, but lack of analysis method. Here we proposed NASTRA, a tool for accurate STR genotyping with nanopore sequencing, which uses an STR-structure-aware algorithm to infer repeat numbers of STR motifs. In our real-time scenario tesing, NASTRA has 100% accuracies for diploid STRs, far exceeding method employing strategy that include all candidate STR allele sequences for alignments. NASTRA could be useful in applications as individual identification and cell-line authentication with nanopore sequencing. NASTRA is available via https://github. com/renzilin/NASTRA.