[bioinfo]DNBSEQ-G400のSEデータtrimming設定（trimmomatic）

trimmomaticのコマンドでハマったのと、初のDNBSEQ且つhiseqを含めてsingle endデータは初めてなのでメモ。

java -jar trimmomatic-0.39.jar SE -threads 16 -phred33 dnbseq_001.fq ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 MINLEN:30

trimmomaticのSE設定で、アダプターはTruSeq3-SE.faBGIの資料にあった下記配列。あとはHiseqデータとほぼ変わらず。標準的な設定。

Primers for BGISEQ/DNBSEQ/MGISEQ library sequencing:
All following sequencing primers are included in the sequencing kits of BGISEQ/DNBSEQ/MGISEQ system.

Read 1 sequencing primer:
GCTCACAGAACGACATGGCTACGATCCGACTT
Barcode SE sequencing primer:
AAGTCGGAGGCCAAGCGGTCTTAGGAAGACAA
Read 2 sequencing primer:
TTGTCTTCCTAAGACCGCTTGGCCTCCGACTT
Barcode PE sequencing primer:
ATGTCGTTCTGTGAGCCAAGGAGTTG

The following sequences are used to filter the adapter contamination in raw data.
Forward filter:
AAGTCGGAGGCCAAGCGGTCTTAGGAAGACAA
Reverse filter:
AAGTCGGATCGTAGCCATGTCGTTCTGTGAGCCAAGGAGTTG