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Wrong Illumina TruSeq adapter sequences in contaminant_list.txt? #52

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aushev opened this issue Jun 30, 2020 · 0 comments
Open

Wrong Illumina TruSeq adapter sequences in contaminant_list.txt? #52

aushev opened this issue Jun 30, 2020 · 0 comments

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@aushev
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aushev commented Jun 30, 2020

I have an impression that sequences of the Illumina TruSeq adaptors starting from Index 13 are wrong. I checked in couple sources, including Illumina website, and starting from Index 13 sequences are different, for example

GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTCAAC  TCTCGTATGCCGTCTTCTGCTTG    # Index 13, current contaminant_list.txt
GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTCAACAATCTCGTATGCCGTCTTCTGCTTG    # Index 13, Illumina file

GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTTCCG  TCTCGTATGCCGTCTTCTGCTTG    # Index 14, current contaminant_list.txt
GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTTCCGTATCTCGTATGCCGTCTTCTGCTTG    # Index 14, Illumina file

(I have added spaces to align easier) You can see that after the 6-letter barcode, there is a 2-letter difference.
Additionally, for Index 23 (

TruSeq Adapter, Index 23 GATCGGAAGAGCACACGTCTGAACTCCAGTCACCCACTCTTCTCGTATGCCGTCTTCTGCTTG
), even the barcode is different: CCACTC in the current contaminant list while GAGTGG in Illumina's list

Overall, maybe it would be helpful to indicate source of information as a comment line before each block of sequences?

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