bbduk

Trim adapters from Illumina sequencing reads

• What are the sequences for the adapters? e.g. ask sequencing provider.
• Get these into their own fasta file, e.g. illumina_adapters.fasta
• Or, use the file that comes with BBTools, that contains all the Illumina adapters for Truseq/Nextera : /bbmap/resources/adapters.fa

Run bbduk:

bbduk.sh in1=/home/reads/R1.fq.gz in2=/home/reads/R2.fq.gz out1=trimmed-readsR1.fastq out2=trimmed-readsR2.fastq \
k=25 mink=8 ktrim=r ref=adapters.fa hdist=1 > bbduk_log.txt

• Note: There may be an error where bbduk tries to uncompress the gz files using bgzip instead of pigz.
• https://sourceforge.net/p/bbmap/tickets/30/
• Option: uncompress files first, or use another tool e.g. fastp

bbudk other flag info for filtering

bbduk.sh in=R1_Acacia.fq.gz in2=R2_Acacia.fq.gz \ 
out=trimmed-readsR1.fastq out2=trimmed-readsR2.fastq \
minlen=50 \ #after trimming, discard reads if this short  
k=25 \ #kmer length  
mink=8 \ #look for shorter kmers at read tips to this min 
ktrim=r \ # trim bases that match adapters, trim to the right
ref=adapters.fa \  #illumina adapters
hdist=1 \ # max hamming distance for reference kmers - num mistmatch allowed 
overwrite=f \ 
qtrim=rl \ # trim R and L ends  at trimq (after kmer search) 
trimq=30 \  # regions with average q below this will be trimmed 
t=auto \ #set to auto so it uses slurm setting
bhist="bhist.txt" \ # Base composition histogram by position. 
qhist="qhist.txt" \ #  Quality histogram by position.
gchist="gchist.txt" \ #  GC content
aqhist="aqhist" \ #  Histogram of average read quality.
lhist="lhist.txt" \ #  Read length histogram.
> "bbduk_log.txt" 

• use supplied adapters.fa file or make your own