What are the adapters in illumina platinium genomes?

Question

[dasdevashishdas]

Hello All,

I want to know the adapters (if present) in the illumina platinium genomes. The website (https://www.illumina.com/platinumgenomes.html) and the paper (http://genome.cshlp.org/content/27/1/157) doesn't talk about it.

Also, is there any specific Cutadapt command, we need to pass to get the correct file for assembly?

[GenoMax]

You can find all common Illumina adapter sequences in the adapters.fa file included in BBMap suite (look in resources directory). While there I encourage you to look at bbduk.sh from BBMap as an alternative for cutadapt that is easy to use/fast.

[Brian Bushnell]

Additionally, for paired-end sequences, you can do this:

bbmerge.sh in1=read1.fq in2=read2.fq outa=adapters.fa

As long as the library has a single pair of adapter sequences (i.e., as long as this is not a mix of multiple libraries with different adapters) this command will give you the consensus adapter sequences for read 1 and read 2 of that library.