Adaptor trimming (best tools)?

Question

[sunnykevin97]

Hi,

May I ask a very basic question. What are the best tools for trimming adapters efficiently.

Little confused. what are the default parameters for trimming adapters using Trimmomatic

Parameters for less sensitive and more sensitive to trim adapters.

I'm working with museum specimens, for genome sequencing (Nextseq-500) PE, we have used only single index libraries. RL - 120 bp, q = 20 & Coverage - 25X.  

Index   Sample
TCCTCA - s1
GTCAGT - s2
CGAATA - s3
TCTAGG - s4
CGCAAC - s5
CGTATC -  s6

Any suggestions please.

Answer 1

[stuart archer]

Cutadapt is my preference, since it also creates output that lets you estimate the proportion of false-positive trimming done, as a function of the length of the match against adapter sequence. (The length of match parameter is probably the most important one to tune for sensitivity vs specificity.) I find it to be transparent in how it operates and the docs are good.

Also I check that the trimming does what I hope it is doing using the Trimviz tool.

[sunnykevin97]

I'm fan of Cutadapt, I totally agree.

Answer 2

[Mensur Dlakic]

In my experience, most companies and/or sequencing centers trim the data before returning it to us. So I would consider that the data might be trimmed already, but would still verify.

Trimming questions get asked probably 5-10 times a week. Searching Biostars for Trimmomatic will give you plenty of material that will explain just about any question you may have. I don't think any program is particularly better than the rest here, as the task is well-defined and straightforward. You may want to consider AdapterRemoval.

Answer 3

[Raman2]

Trimmomatic and fastp helps trimming the reads. For paired end data, you have to provide the adapter sequence to be trimmed

Answer 4

[Soheil]

I prefer Trim Galore which is a wrapper around Cutadapt and FastQC