Pipeline overview

Optional preliminary steps

• Convert to new format
• Merge forward and reverse reads

Middle steps

• Remove primers
• Quality filter (depends on removed primers fastq)
• Dereplicate (depends on quality filtered fasta)
• ?? demultiplex
• Make an index file (depends on dereplicated fasta and quality-filtered fasta)
• Make a sequence table (depends on quality filtered fasta)

OTU calling

• Calling OTUs (depends on dereplicated fasta)
• Make an OTU table (depends on index file and uc files from OTU calling)