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need to warn the user if he deblurs using trim longer than the run read length (i.e. -t 150 and the sequencing is 100bp long)
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Looking at some of the taxonomy metadata, the last few characters are cropped off. Here is an example of such a taxonomy string.
```
['k__Bacteria', 'p__Proteobacteria', 'c__Alphaproteobacteria', …
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Right now, this pipeline only takes in fasta files. Is there any interest in reading from fastq instead?
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just need to change the one import for stringio to include if version
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Strongly recommend removing biom 1.x format support and requiring h5py.
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positive (gg 88% rep set) and negative (phix+adapter) fasta files are a part of the git
need deblurring to access them by default based on the mode (-n)
also need to test if not indexed, index them (1…
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Its not clear exactly what dependencies are required to run this.
After talking to @josenavas, I realized that MAFFT and SortMeRNA are required.
What other dependencies are required? The documentati…
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See [here](https://github.com/biocore/scikit-bio/pull/53#discussion-diff-9171472)
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From @acardona:
> When opening the ClearVolume Network Client the whole JVM segfaults:
>
> ```
> #
> # A fatal error has been detected by the Java Runtime Environment:
> #
> # SIGSEGV (0xb) at pc=0…