Removing Illumina Single End PCR Primers and TruSeq Adapters

Question

[serpalma.v]

Dear community

I have 1080 FASTQ files and I've run them all through FastQC to evaluate their quality.

Then I aggregated the output with the R package fastqcr, which also allowed me to identify distinctingly the sequences found in the module "Overrepresented Sequences". Thus, accross all 1080 files these are the sequences giving troubles:

 [1] "ATCGGAAGAGCACACGTCTGAACTCCAGTCACACTGATATATCTCGTATG TruSeq Adapter, Index 25 "        
 [2] "ATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGT Illumina Single End PCR Primer 1 "
 [3] "ATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGCC TruSeq Adapter, Index 4 "         
 [4] "GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGC TruSeq Adapter, Index 4 "         
 [5] "ATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAAACTCGTATGCC TruSeq Adapter, Index 4 "         
 [6] "GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG Illumina Single End PCR Primer 1 "
 [7] "ATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCC TruSeq Adapter, Index 7 "         
 [8] "ATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCAACTCGTATGCC TruSeq Adapter, Index 7 "         
 [9] "ATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCAGCTCGTATGCC TruSeq Adapter, Index 7 "         
[10] "ATCGGAAGAGCACACGTCTGAACTCCAGTCACGTTTCGGAATCTCGTATG TruSeq Adapter, Index 21 "        
[11] "ATCGGAAGAGCACACGTCTGAACTCCAGTCACCCGTCCCGATCTCGTATG TruSeq Adapter, Index 16 "        
[12] "ATCGGAAGAGCACACGTCTGAACTCCAGTCACATGTCAGAATCTCGTATG TruSeq Adapter, Index 15 "        
[13] "ATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCC TruSeq Adapter, Index 1 "         
[14] "ATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGTGGATATCTCGTATG TruSeq Adapter, Index 7 "         
[15] "ATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCC TruSeq Adapter, Index 6 "         
[16] "ATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAATCTCGTATGCC TruSeq Adapter, Index 12

To remove the adapters and primers I need to find the correct file to pass on to i.e. Trimmomatic.

Where could I find such file?`

I have gone through several threads and blog posts, but all of them point out the TruSeq Adapters, and I cannot find one with all the corresponding oligos for my sequencing chemistry (I have only been told that the libraries were prepared using TruSeq Nano).

Thanks in advance!

Answer 1

[GenoMax]

You can also use bbduk.sh from BBMap suite. BBMap software includes adapters.fa in resources directory that contains all commonly available adapter kit sequences. Guide for bbduk is available here.

Answer 2

[finswimmer]

Hello,

trimmomatic provides an adapter file. In my system these are located under /usr/share/trimmomatic as I've installed via package manager.

$ ls /usr/share/trimmomatic/           
NexteraPE-PE.fa  TruSeq2-PE.fa  TruSeq2-SE.fa  TruSeq3-PE-2.fa  TruSeq3-PE.fa  TruSeq3-SE.fa

But you can create your own file containing the adapter sequences. It's a normal fasta file:

$ cat /usr/share/trimmomatic/TruSeq3-SE.fa 
>TruSeq3_IndexedAdapter
AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
>TruSeq3_UniversalAdapter
AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA

fin swimmer