What do the FASTQ file names mean here? I would like to run an analysis on Nanopore data. I'm trying to download sample data from https://github.com/nanopore-wgs-consortium/chm13. I would like to run minimap on the FASTQ files, resuling in a single BAM file.



Q: What do the file names mean? What is "S13"? What is "L002_l1"? What is "L002_R1"? Am I supposed to download them and combine them into a single FASTQ file, and then align them?
What is "S13"?

S# is most likely the sample number. If so, you do not want to combine these.

What is "L002_l1"? 

L00# is the lane number (of the 8 Illumina flow cell lanes). 'I1_' (not 'L') are index files and are not needed (see also https://www.biostars.org/p/374581/).

What is "L002_R1"?

R1 is one end of paired-end sequencing, R2 is the other end. These filepairs must have the same number of lines. Use an aligner that utilizes both.