BBTOOLS COMMANDS
----------------

readlength.sh in=reads.fq

# May not work depending on version

# shred.sh in=reads.fq out=shredded_50_100.fq length=100 minlength=50
# readlength.sh in=shredded_50_100.fq

reformat.sh in=reads.fq out=trimmed.fq ftr=19

reformat.sh in=trimmed.fq out=gc_filtered.fq mingc=0.5

reformat.sh in=qc_filtered.fq out=100_reads.fq sample=100 bhist=bhist.txt qhist=qhist.txt aqhist=aqhist.txt lhist=lhist.txt qchist=gchist.txt

## For the next command you will need to download the phiX genome to your usr directory and change the path for ref=/ to the download location

wget http://evomicsorg.wpengine.netdna-cdn.com/wp-content/uploads/2015/12/phiX_genome.txt

bbduk.sh in=reads_new.fq out=phix_removed.fq ref=/mnt/data1/databases/contaminants/phix174_ill.ref.fa.gz

## Deduplicate reads

dedupe.sh in=phix_removed.fq out=deduped.fq csf=cluster.stats minidentity=95