memory requirements for alignment
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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.

24-Nov-2016
UPARSE tutorial video posted on YouTube. Make OTUs from MiSeq reads.

 

USEARCH v11

memory requirements for alignment


See also
 
Reducing memory
 
32-bit and 64-bit binaries

  Memory requirements for a database index

The amount of memory required to align a pair of sequences scales like the product of the sequence lengths. In the worst case, approximately 4NM bytes may be needed, where N and M are the sequence lengths. For very long sequences, say 20k or more, this can be a lot: 4 x 20k x 20k = 1.6 Gb.