QIIME map file
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11-Aug-2018 New paper describes octave plots for visualizing alpha diversity.

12-Jun-2018 New paper shows that one in five taxonomy annotations in SILVA and Greengenes are wrong.

18-Apr-2018 New paper shows that taxonomy prediction accuracy is <50% for V4 sequences.

05-Oct-2017 PeerJ paper shows low accuracy of closed- and open-ref. QIIME OTUs.

22-Sep-2017 New paper shows 97% threshold is wrong, OTUs should be 99% full-length 16S, 100% for V4.

UPARSE tutorial video posted on YouTube. Make OTUs from MiSeq reads.



QIIME map file

QIIME maps are tab-separated text files used to store an OTU table. This format is generated by the pick_closed_reference_otus.py and pick_open_reference_otus.py scripts, which also generate OTU tables in BIOM format.

The qiimemap2otutab command converts a QIIME map file to QIIME classic format.

With pick_closed_reference_otus.py, the map file is dir/uclust_ref_picked_otus/name_otus.txt, where dir is the directory name specified by the -o option and name is the input file name (truncated by rules that are not quite clear to me, e.g. the filename extension is deleted). With pick_open_reference_otus.py, there are two map files: dir/final_otu_map.txt and dir/final_otu_map_mc2.txt. The first contains all reads. The second has singleton OTUs deleted (mc2 means "minimum count 2").

Each line in the file represents one OTU. For closed-reference OTUs, this is an integer accession number from the GG97 database. The OTU identifier is followed by a tab-separated list of read labels. Each read label starts with the sample name followed by an underscore and the read number.

Example QIIME map file