adapter4srna

Adapter in small RNA sequencing

This is an open access reporitory to collect all used adapter sequences in currently commercial available and discontinued kits.

Any comments and contributions are welcomed.

3' adapter for small RNA sequencing on Illumina platform

Vendor	Kit	Version	3' Adapter sequence
New England Biolabs	NEBNext Multiplex Small RNA Library Prep Kit for Illumina	V3	5'-AGATCGGAAGAGCACACGTCT-3'
Illumina	TruSeq Small RNA	Version	5’-TGGAATTCTCGGGTGCCAAGG-3'
PerkinElmer	NEXTflex Small RNA Sequencing Kit **	V3	5’-TGGAATTCTCGGGTGCCAAGG-3'
Qiagen	QIAseq miRNA Library Kit	Version	5’-AACTGTAGGCACCATCAAT-3'
Lexogen	Small RNA-Seq Library Prep Kit	Version	5’-TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC-3'
SeqMatic	TailorMix miRNA Sample Preparation Kit	V2	5’-TGGAATTCTCGGGTGCCAAGG-3'
Takara	SMARTer smRNA-Seq Kit for Illumina	Version	5’-AAAAAAAAAA-3'
TriLink	CleanTag Small RNA Library Prep Kit	Version	5'-TGGAATTCTCGGGTGCCAAGG-3'
Diagenode	CATS small RNA-seq Kit	Version	5'-GATCGGAAGAGCACACGTCTG-3'
GenXPro	TrueQuant SmallRNA Seq Kit for Ultra Low Input	Version	TODO
Epicentre	ScriptMiner Small RNA-Seq Library Preparation Kit	Version	~~ ~~
Life Technology	SREK, Small RNA Expression Kit	version C	~~ ~~

**4 random bases

Kit Discontinued kit

CATS Small RNA sequencing kit for Illumina

Version 2 | 01.17

cutadapt -u 3 input_file.fastq | cutadapt -a AAAAAAAA - | cutadapt -a AAAAAAAN$ -a AAAAAAN$ -a AAAAAN$ - | cutadapt -a AGAGCACACGTCTG - | cutadapt -O 8 -g GTTCAGAGTTCTACAGTCCGACGATCNNN - | cutadapt -m 18 -o output_file.fastq -

Version 2 | 03.17

cutadapt -u 3 input_file.fastq | cutadapt -a AAAAAAAA - | cutadapt -a AAAAAAAN$ -a AAAAAAN$ -a AAAAAN$ - | cutadapt -a AGAGCACACGTCTG - | cutadapt -O 8 -g GTTCAGAGTTCTACAGTCCGACGATCNNN - | cutadapt -m 18 -o output_file.fastq -

Version 2 | 09.17

cutadapt --trim-n -a GATCGGAAGAGCACACGTCTG -a AGAGCACACGTCTG <input.file> | cutadapt -u 3 -a A{100} --no-indels -e 0.16666666666666666 - | cutadapt -O 8 --match-read-wildcards -g GTTCAGAGTTCTACAGTCCGACGATCSSS -m 18 -o <output.file> -

Contributing

Any comments and contributions are welcome. Pull requests are welcome.