which sequence adapter trimming tool should i use for my illumina 101pb reads ?

Question

[v.berriosfarias]

Hello, I want to trim adaptor sequences from my raw reads, the report data of the sequencer company details that adapters were not removed from the reads but do not detail the adapter sequence used, so I took a look to the library kit used and it was the Truseq DNA-PCR free kit from Illumina. then I went to the page https://support.illumina.com/bulletins/2016/12/what-sequences-do-i-use-for-adapter-trimming.html and it seems that I must use this sequence for trimming my paired-end reads:

Illumina DNA PCR-Free Prep, Tagmentation CTGTCTCTTATACACATCT+ATGTGTATAAGAGACA

I checked that "tagmentation" was part of the procedure.

with this, what does the "+" means in that sequence? which tool should I use for trimming those adapter sequences?

I saw that the above sequence must be used for both read 1 and read 2 of a paired-end run but how can I know if the adapters are on the 5´ end or 3´end of the respective reads? If helps the report data describes that in the library preparation procedure adapters were ligated 5´end and 3´end The read´s length is of 101pb for each read.

Answer 1

[Jiacheng]

I'd recommend atria to determine and trim the adapter sequences. It is a newly-published cutting-edge trimmer with exceptional precision and speed. And if you do not know what adapter sequence should be used, Atria can detect adapters if adapter content is higher than 0.04%. (If <0.04%, no need to do adapter trimming.)

Eg: Finding adapters for R1 and R2

atria --detect-adapter -r read1.fastq -R read2.fastq

Adapter trimming

atria -r read1.fastq -R read2.fastq -a ADAPTER_READ1 -A ADAPTER_READ2

Answer 2

[swbarnes2]

It's probably easiest to use fastqc to assess what adapters might or might not be present. It might not be a problem.

[v.berriosfarias]

yes I used fastqc to assess if there were any adapter sequences, and no adapter was shown, but it seems that fastqc doesn't recognize the adapters, the report data of the raw reads says that "adapters were not trimmed" , there must be adapters sequences in those reads and it so frustrating that the report data doesn't bring the adapter sequences, neither if they are on 5´or in 3´