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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 minimap2 on the FASTQ files, resulting in a single BAM file.

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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?

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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.

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Peter's answer is a good one and to the point. I'll be a bit more verbose.

The breakdown of FASTQ file names that come directly from the sequencer typically have the following format:

{sample_name}_S{sample number}_L{lane number}_{R/I}{read or index number}_001.fastq.gz

sample_name is the sample name provided by you (or whoever sequenced the data) to the sequencer.

To save time and money, samples are often "multiplexed" on sequencing runs. This multiplexing means you aggregate samples ("S") on the same run and split samples on different lanes ("L") to limit some technical noise. Lanes are essentially technical replicates for the sequencing data on the same sequencing run, and these numbers tell you which sample and which lane that FASTQ comes from.

Sequencing can be done in single-end or paired-end. Single-end sequencing generates a single FASTQ file (_R1), whereas paired-end sequencing produces 2 FASTQ files (_R1 and _R2).

The data you highlight isn't actually Nanopore:

Approximately 50x of data was generated on a NovaSeq instrument.

10x includes "indexes" ("I") in addition to the sample and lane information to keep track of things like single cells or other unique molecular identifiers, and that information is listed after the I. _R1, _R2, and _I1 all go together for a unique sample and lane combination

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The file names mean this isn't Nanopore data. Read the bit just above these file names:

Approximately 50x of data was generated on a NovaSeq instrument. Based on the summary output of Supernova, there are 1.2 billion reads with 41x effective coverage.

That linked github page has Nanopore, Illumina/10x, BioNano, HiC, and PacBio data. For the nanopore files, you should be looking at this section.

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