Does illumina_adapters_all.fasta have the Nextera adaptors?

Question

Does illumina_adapters_all.fasta have the Nextera adaptors?

Closed this issue 10 years ago · 3 comments

Does illumina_adapters_all.fasta have Nextera adaptors in it?

Answer 1 · 2015-06-14T03:05:54.000Z

Not sure, I never deal with nextera libraries.

Answer 2 · 2015-06-14T06:43:47.000Z

If you ever get sequence from MiSeq or NextSeq (and soon HiSeq) they will have used Nextera rather than TruSeq. With luck, they will be pre-removed by the Illumina base caller, but often not. Will screw up your assemblies.

Here's the trimmomatic file for them:

>PrefixNX/1
AGATGTGTATAAGAGACAG
>PrefixNX/2
AGATGTGTATAAGAGACAG
>Trans1
TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG
>Trans1_rc
CTGTCTCTTATACACATCTGACGCTGCCGACGA
>Trans2
GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG
>Trans2_rc
CTGTCTCTTATACACATCTCCGAGCCCACGAGAC

Answer 3 · 2015-06-14T15:54:03.000Z

Thanks, I added in the ones that weren't there already.