whole genome sequencing and assembly

Question

[manaswiniparija3]

we extracted the whole genome of a fish and went for short-read sequencing using an MGI sequencer. usually, when we get sequencing results we get two files one fastq for forward and one fastq for reverse. but in my case, we got several fastq files of different sizes. can anyone explain what are these multiple files and how we can do an assembly out of them?

[DBScan]

How do your files look like? My guess is they were split by lane and/or flowcell.

[manaswiniparija3]

yes, I got 4 different lanes in 4 different folders. inside each lane, multiple fastq files are there.

[manaswiniparija3]

[DBScan]

Then you can align each combination separately and then merge the BAMs. For instance, align

• "FLOWCELL_L001_R1_001.fastq.gz" and "FLOWCELL_L001_R2_001.fastq.gz" together
• "FLOWCELL_L002_R1_001.fastq.gz" and "FLOWCELL_L002_R2_001.fastq.gz" together,

and so on.

[manaswiniparija3]

can you say me why multiple fastq files were generated?? is it because the sample was uploaded in different flowcells and from different flowcells different fastq were generated? and does all the flowcell contains data from the same sample?