Question: Why Does The Base Quality Drop Towards The End For Illumina Reads ?
4
gravatar for jack
3.9 years ago by
jack390
jack390 wrote:

Does anybody knows why, why base quality drops towards the end for Illumina reads ?

bioinformatics illumina • 5.4k views
ADD COMMENTlink modified 22 months ago by andrew.j.skelton734.1k • written 3.9 years ago by jack390
1

Good question - I have always accepted the phenomenon without really understanding the cause.

ADD REPLYlink written 3.9 years ago by Ian5.0k
9
gravatar for Istvan Albert
3.9 years ago by
Istvan Albert ♦♦ 75k
University Park, USA
Istvan Albert ♦♦ 75k wrote:

The illumina platform uses a so called sequencing by synthesis process. Bases are added one at a time and the consensus is determined in a cluster of identical sequences.

The source of errors can be numerous, here is one review that discusses the issues in more detail:

The challenges of sequencing by synthesis, Nature Biotech, 2009

In a nuthsell a short answer to the best of my understanding is this: Not all sequences in a cluster will grow at the same rate, this will slowly lead to a desynchronization as the errors accumulate. This is why the quality dips towards the end.

ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by Istvan Albert ♦♦ 75k
1
gravatar for zcenio34
22 months ago by
zcenio34100
Germany
zcenio34100 wrote:

See this post:

Why does base quality of reads generally decreases at the end of the read? 

ADD COMMENTlink written 22 months ago by zcenio34100
0
gravatar for andrew.j.skelton73
22 months ago by
Newcastle Upon Tyne
andrew.j.skelton734.1k wrote:

I'd highly recommend you check out this - The site as a whole is useful for explaining common things you'd see in sequencing, like primer bias. 

ADD COMMENTlink written 22 months ago by andrew.j.skelton734.1k

Link looks broken, can you check?

ADD REPLYlink written 21 months ago by zcenio34100

Seems to be down at the moment

ADD REPLYlink written 21 months ago by andrew.j.skelton734.1k
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