ghost-tree

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Update Python version for ghost-tree compatibility with QIIME 2 2019.1 release

2

ghost-tree updates for QIIME 2019.1 release * Fix flake8 code errors in Python 3.6 build (flake8 checks for Python Pep8 style) * Remove Python 3.4 support, fix 3.6 support and...

JTFouquier

Build new 2018 UNITE ghost trees & sign up for a notification somehow for when there are new UNITE databases released.

JTFouquier

Update readme to include pictures; refs to QIIME 2 analysis steps See QIIME 2 community tutorial

JTFouquier

ghost_tree_extension_accession_ids.txt ghost_tree_tips.txt These files should be renamed for consistency. This was understandably unclear to a user.

JTFouquier

Select the longest sequence within each genus

1

Hello Jennifer! I’m glad that you plan to improve `ghost-tree`! I would like to add another enhancement request to the list. Currently, for each genus `ghost-tree` takes the first sequence...

vmikk

Now that QIIME 1 is no longer supported, there is no need to have documentation to help people use QIIME 1.

JTFouquier

Analyze the effect of clustering at lower percent similarity with 'extensions-cluster' (loss of accuracy vs loss of samples). If you did not discard many seqs without the clustering step, then...

JTFouquier

For fun, allow people to print their tree using ascii art. Just a simple option, but need to warn them about the size, OR check for size.

JTFouquier

This is not too big of a deal as currently selecting 'genus' is a liberal option. But if people are interested in collapsing at higher ranks, which are less well...

JTFouquier

Remove dependency on OTU picking

2

Qiime2 does not require OTU picking as research has evolved/improved. Remove the dependency/requirement of an OTU map as an input to ghost-tree. Consider making it an option. Revisit Jai and...

JTFouquier