neufeld / axiome Goto Github PK

Rather than just produce the concordance graph, it should do some point-of-inflection magic to determine what degrees the user should try (possibly writing them back into the original .aq file).

Implement similar filtering to the http://qiime.org/scripts/filter_otus_from_otu_table.html script.

Currently, for OTU picking we support QIIME's cdhit and uclust methods, and raw cdhit and uclust calls (going around QIIME in case of memory issues).

There are many other options which need to be added in to AutoQIIME. Additionally, we need to support some kind of arbitrary "additional flags" parameter so that users can pass any of the many arguments for pick_otus.py to their AutoQIIME pipeline.

QIIME has multiple scripts to do classification, but we only support RDP.

We need to add in a classification parameter to specify the other QIIME methods.

Many steps (and QIIME scripts) now support multiple cores. It should be investigated which steps support multiple cores, and add in an option to utilize them.

Currently, only PANDAseq can use multiple cores by setting the environment variable PANDA_FLAGS="-T #" where # is the number of cores you would like PANDAseq to use.

Currently, the pipeline takes in plain FASTA files, and Illumina paired end sequence data (via PANDAseq). We need to add support for 454 data format, including a denoising step.

This can be done manually at the moment by following this guide:
http://qiime.org/tutorials/denoising_454_data.html

Instead of running pick_otus.py on the resulting denoised_seqs.fna file, you should instead use that as a FASTA input to AutoQIIME.