Importing/converting (.SFF) to (FASTA, QUAL ,flowgram) using QIIME2

[tlaw (T)]

I am looking to import and convert sequencing data (.SFF file format) generated by the Roche 454 GS-FLX+ Genome Sequencer using QIIME2. Previously this was done in QIIME using the ‘process_sff.py’ script (http://qiime.org/scripts/process_sff.html). Is this still the same for QIIME2? Are there any tutorials/descriptions on how this is done in QIIME2?

[pjtorres (Pedro J. Torres)]

Hi @tlaw,

Currently, as far as I know, QIIME 2 does not support 454 data. If you want to use denoising algorithms I know you can use DADA2 but not in QIIME2. Your best option would probably be to use a different tool to process your data, like DADA2 or QIIME1, and once you have a biom file you can import this to QIIME2.

[thermokarst]

Thanks @pjtorres! @tlaw, we don’t currently support 454 data, but as @pjtorres suggests, you could process these data with QIIME 1 and then import into QIIME 2, if you are looking to get moving on analysis now. Otherwise, we will update this forum post as we begin to provide direct 454 support in QIIME 2. Thanks!