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.
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.