illumina sequencing

[mido1951]

Hello friends,

I want to know the illumina sequencing method.
in DNA there are two strands (double helix) and illumina generates two F1.fq file and F2.fq.
Do F1.fq means sequencing of the first strand of DNA and the second is the sequencing of the second strand (the complement of the first)?
thank you for your explanations

[GenoMax]

Yes. See this simplified video for an explanation.

https://www.youtube.com/watch?v=HMyCqWhwB8E

[mido1951]

Genomax thank you.
I understood the video but there are things that are not clear because I'm not biologist.
i have two files from illumina sequencing.
for example:
my first sequence in F1.fq is: AACCTGTCTCACGACGG...
and the second in F2.fq is: AAGCGGAGCTGGNNTT....
I know "Is a basic ambiguous but it is the complement of F1.fq?
from what I see is not the complement

another question please:
if F1.fq is the first Strand of DNA and the F2.fq its complement.
in the assembly tools, why we use two files to assemble (F1.fq and F2.fq)? when you can use one file
I'm no expert but just a question.
thankyou

[GenoMax]

You are sequencing fragment(s) from the two ends.

F1 (or R1) samples the first X bp from the first strand (depending on number of cycles used). F2 (or R2) samples the first X bp from the complementary strand on the same fragment. So F1/R1 and F2/R2 are not necessarily complementary over their entire length (as long as the fragment being sequenced is > length of read).

With longer read lengths (2 x 300 bp) it is possible to have some overlap in the middle. In this case the two reads (R1/R2) can be stitched together to create an artificial longer read (BBMerge/FLASH are programs that do this merging). Part that overlaps in the middle is used to create a consensus.