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Topics in sequence analysis

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OTU analysis   Defining and interpreting OTUs   Interpreting counts and frequencies in an OTU table   Read abundances do not correlate with species abundances!   Mapping reads to OTUs   Quality control for OTU sequences   Abundance bias   Cross-talk   Chimeras   Problems with closed- and open-reference OTUs   Comparing two sets of OTUs for the same reads   2x250 PE can sequence more than V4   For best results, pool all samples together Clustering methods   Greedy clustering   Agglomerative clustering   Connected components   Clustering metagenomics contigs   Clustering by local alignment   Taxonomy   Defining accuracy for taxonomy classifiers   Confidence measures for taxonomy predictions

Diversity analysis   Alpha diversity   Beta diversity   Rarefaction   Effective number of species Next-generation reads   Quality filtering   Expected errors   Quality (Phred) scores   Average Q scores are a bad idea   Should you increase max e.e. for long reads?   Denoising 454, PacBio and Ion Torrent reads   Paired-read assembly   Cross-talk between multiplexed samples Miscellaneous   Defining unique sequence abundance   Masking low-complexity sequences   NAST multiple alignments   PCR amplicon prediction