sequencing machines output files layout

Question

[hamarillo]

Hi!

Does anyone know if someone has created a resource or gathered information about which type of layout each sequencing machine produces?

Some table or something where one can look up a sequencer model, say "NextSeq 500" and there's information about the resulting layout i.e. "4 lanes" so people will know its 4 PE FASTQ files and can code analysis workflows easier or is it really like everyone is doing their own experimental configurations and loading their samples with as many indexes as possible and you could end up with weird and specific layouts each time?

thanks

Answer 1

[GenoMax]

This is not simple to answer. "Specifications" section on Illumina website for each sequencer they sell is a good start. Here is an example for NovaSeq 6000: https://www.illumina.com/systems/sequencing-platforms/novaseq/specifications.html

In General:

iSeq - I assume it is one channel/lane
MiSeq/MiSeqDX - one lane
HiSeq 2500/3000/4000- 2 lanes or 8 lanes (depending on type of flowcell and run)
NextSeq 500/550 - Even though there are 4 "lanes" they are not fluidically independent (so there is one physical channel). Only one pool can be used across 4 "lanes"
NovaSeq 6000 - 1, 2 or 4 lanes depending on flowcell (XP kit required to use lanes independently)
NovaSeq X - Someone else will fill in.

At the end of the day, each sample should minimally have one file (single-end) or one pair of files (paired-end). If the sample ran on multiple lanes then there may be lane specific files (designated by L001, L002 etc in the file name). It is possible to process the data in such as way that no lane-specific files are produced, even if the sample ran on more than one lane.

Answer 2

[swbarnes2]

Not all nextsrq runs are PE. You can also generate fastqs which combine all the lanes.