Anna Syme

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Trim adapters from Illumina sequencing reads

Run bbduk: 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

bbudk other flag info for filtering 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"