What are the adapters in illumina platinium genomes?
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?
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You can find all common Illumina adapter sequences in the
adapters.fafile included in BBMap suite (look inresourcesdirectory). While there I encourage you to look atbbduk.shfrom BBMap as an alternative for cutadapt that is easy to use/fast.Additionally, for paired-end sequences, you can do this:
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.