qiime
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biocore
Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.
UCLUST/USEARCH cluster slowly at identities far from 0.97 (i.e. the 0.60 setting used for prefiltering with open-ref OTU picking). Currently, the pick_open_reference_otus.py script does a prefilter at 0.60 (parallelized) for...
First is that the workflow incorrectly names the alignment output directory (notice that it is still called `pynast_aligned_seqs`: ``` align_seqs.py -i OTUS//rep_set.fna -o OTUS//pynast_aligned_seqs --alignment_method muscle ``` Second is that,...
I've been working on several data sets lately looking at community change before/after a treatment, and have been working on [some code](https://gist.github.com/gregcaporaso/79dc526708b1e739ea8d) for testing whether some _value of interest_ changes...
QIIME should import all command line interface and command line interface testing functionality from [qcli](https://github.com/bipy/qcli) rather than PyCogent. - [x] update imports from scripts (this is easy as only util.py...
Currently pick_de_novo_otus.py and pick_closed_reference_otus.py force users to pass a parameters file to change the otu picking method, but pick_open_reference_otus.py allows users to pass that on the command line. Update the...
subsampled open reference otu picking gives traceback if no sequences are discarded by the prefilter
pick_open_reference_otus.py -i $PWD/seqs1.fna -r $PWD/refseqs.fna -o $PWD/ucrss_usearch/ -s 0.1 -p $PWD/ucrss_params.txt -m usearch61 -v Pick Reference OTUs (prefilter) pick_otus.py -i /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/seqs1.fna -o /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/ucrss_usearch//prefilter_otus/ -r /Users/caporaso/code/Qiime/qiime_test_data/pick_open_reference_otus/refseqs.fna -m usearch61_ref --similarity 0.6 --enable_rev_strand_match...
When the workers fail due to memory (this is the only case I have encountered but not sure if other exist) the main job still collects the resulting and incomplete...
