# Quality filter and trim reads
$ QualityFilt.pl seqs.txt > seqs_qf.txt

# Captures reads with specific barcode
$ BarcodeSplit.pl seqs_qf.txt XXXXXXTGCAGG > seqs_qf_Sample1.txt
$ BarcodeSplit.pl seqs_qf.txt XXXXXXTGCAGG > seqs_qf_Sample2.txt
$ BarcodeSplit.pl seqs_qf.txt XXXXXXTGCAGG > seqs_qf_Sample3.txt

# Hash sequences
$ HashSeqs.pl seqs_qf_Sample1.txt Sample1 > seqs_qf_Sample1.hash
$ ...

# Concatenate hash files
$ cat seqs_qf_Sample1.hash seqs_qf_Sample2.hash seqs_qf_Sample3.hash > seqs_qf_SampleX.hash  

# Create novoalign index
$ novoindex seqs_qf_SampleX seqs_qf_SampleX.hash

# Perform all-by-all alignment with novoalign
$ novoalign -r E 20 -t 250 -d seqs_qf_SampleX -f seqs_qf_SampleX.hash > seqs_qf_SampleX.novo

# Place sequences into discrete loci
$ IdentifyLoci.pl seqs_qf_SampleX.novo > seqs_qf_SampleX.loci

# Filter polymorphic loci
$ FilterLoci.pl seqs_qf_SampleX.loci > seqs_qf_SampleX_polymorphic.loci