How to Align one fastq with reference using HISAT2

[sekhwal]

Hi, I have one fastq file (MinION) and a reference file. I am looking to align these. Please suggest a example command to perform the analysis.

This is my fastq file format.

@ID_37312 ATTGTTGCGCTGTTAGAATTTAAAAGATTTGATTCCTTACCAATAATTATTTTTTCCGCATTAATTTCAATAGCAGAACAAATTTTGTTATTTTTAAAAC + AAFFAFFJJJ7AFJJJFFAFJJFJJFAJ-F7JFJ<FJJJ7FFJFFJJJ7FAJFJJJJJJFJJJJF--FAFJJFJJFJF<JJJJJJJJ<FFA7A<FJJJJ< @ID_37313 ATTGTTGCGCTGTTAGAATTTAAAAAAGAAATAATTCGTAGATATTACCCAACAATAGTGAATTATCAACAAGATAAGACTCCAAAAAGTTATGTTAATC + AAFFFFFJJJFJJAFJ7<FJ<AFFFJFJ<FJJFFJJJJJJ<AJJFJFJ7-<AFAF<AJFJAA7FFJF<JJFJFFJFFFFFAFF<FFJFF<<FAFJJFFJF

Thank you,