Merge 0820f8d into 7d4ad95

Author: antgonza

CHANGELOG.md

@@ -3,6 +3,7 @@
 Version 2021.09
 ---------------
 
+* Updated the qp-deblur plugin to version 2021.09; [more information](https://qiita.ucsd.edu/static/doc/html/processingdata/deblur_2021.09.html).
 * Double the number of possible connections for the Qiita database: 100 -> 200 simultaneous connections.
 * Added a new data type: "Job Output Folder" and artifact type definition: "job-output-folder" to initially support admin-only standalone commands in Qiita.
 * The study listing is now sorted by descending study id and then ascending number of available artifacts.

qiita_pet/support_files/doc/source/processingdata/deblur2021.09_private_public.png

@@ -0,0 +1,42 @@
+deblur version 2021.09
+======================
+
+The deblur version 2021.09 addresses a bug with the fragment insertion parsing and
+cache that ignored some fragments for getting an accurate placement in the tree. In
+summary, in some occasions SEPP will return multiple fragments in a single entry; which
+was unexpected by the qp-deblur plugin parser, which assumed only one entry - the
+extra features will be seen as missing by the plugin and that information was
+sent and stored in the cache provided by Qiita, then propagated to future studies and
+meta-analyses.
+
+This bug was resolved in this `pull request <https://github.com/qiita-spots/qp-deblur/pull/60>`__.
+
+Sample counts implications
+--------------------------
+
+At the time of writing Qiita had 978,052 16S deblured private or pubic samples.
+In the figure below, we have at different trimming lengths how samples we will recover
+based on the minimum number of sequences per sample - this is an important consideration
+as we normally need to remove samples below a given threshold for beta diversity
+calculations (via rarefactoin) or differential abundance testing.
+
+.. figure::  deblur2021.09_private_public.png
+   :align:   center
+
+A few conclusions from this plot:
+
+- The maximum number of samples that we will recover are 6,771 at `Trimming (length: 150)`
+  and min_seqs of 1,500; which represents a 0.7% increment in private and public samples.
+- At all Trimming lengths the curve tends to go up at up and then down based on min_seq,
+  which is a common trend seen in rarefacion plots
+
+
+Reaching out to affected study owners
+-------------------------------------
+
+As you saw in the previous section the effect of the missing fragments depends on the
+study, the trimming length and the minimal sequence count per sample selected. As a
+general rule of thumb, as a first analytical pass for meta-analysis for 16S data, we use
+5,000 sequences per sample and we prefer 150 base pair trimming. Thus, we directly
+contacted all study owners that would recover more than 5% of the samples in their study
+(total 24).

qiita_pet/support_files/doc/source/processingdata/deblur_2021.09.rst

@@ -172,6 +172,7 @@ Looking for information about debluring? Please see the document here:
 .. toctree::
 
    deblur_quality.rst
+   deblur_2021.09.rst
 
 Closed-Reference OTU Picking
 ----------------------------