Illumina adaptor trimming

### NGB00362.1:1-61 Illumina Paired End PCR Primer 2.0
perl -p -i -e 's/AGATCGGAAGAGCGGT.*//' z-trim-test.trim
perl -p -i -e 's/AGATCGGAAGAGCGG$//' z-trim-test.trim

### NGB00361.1:1-92 Illumina PCR Primer
perl -p -i -e 's/AGATCGGAAGAGCGTC.*//' z-trim-test.trim
perl -p -i -e 's/AGATCGGAAGAGCGT$//' z-trim-test.trim

### Common region for Illumina PCR Primer and Paired End PCR Primer 2.0
perl -p -i -e 's/AGATCGGAAGAGCG$//' z-trim-test.trim
perl -p -i -e 's/AGATCGGAAGAGC$//' z-trim-test.trim
perl -p -i -e 's/AGATCGGAAGAG$//' z-trim-test.trim
perl -p -i -e 's/AGATCGGAAGA$//' z-trim-test.trim
perl -p -i -e 's/AGATCGGAAG$//' z-trim-test.trim
perl -p -i -e 's/AGATCGGAA$//' z-trim-test.trim
perl -p -i -e 's/AGATCGGA$//' z-trim-test.trim

Removing of homopolymer tails:

perl -p -i -e 's/^A{8,}//' z-trim-test.trim
perl -p -i -e 's/^T{8,}//' z-trim-test.trim
perl -p -i -e 's/^C{8,}//' z-trim-test.trim
perl -p -i -e 's/^G{8,}//' z-trim-test.trim

perl -p -i -e 's/A{8,}$//' z-trim-test.trim
perl -p -i -e 's/T{8,}$//' z-trim-test.trim
perl -p -i -e 's/G{8,}$//' z-trim-test.trim
perl -p -i -e 's/C{8,}$//' z-trim-test.trim