importing fasta file from PacBio

colinbrislawn · December 5, 2019, 2:39pm

Good morning @binzuo

Welcome to the forums!

I have some bad news for you; long PacBio reads are supported by dada2 1.10, but they are not yet supported by the Qiime2 plugin.

But we are working on it! You can keep track of our progress here:

github.com/qiime2/q2-dada2

Add long-read support

opened 09:17PM - 20 Sep 18 UTC

closed 08:50PM - 15 Nov 22 UTC

benjjneb

**Improvement Description** Add long-read support **Current Behavior** We'v…e added support for PacBio long-read amplicon sequencing to the devel version of the R package and it seems to work quite well. Preprint: High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution. **Proposed Behavior** I think it will make sense to add this as a tech-specific ```denoise-pacbio``` command in the plugin. This is similar to the ```denoise-pyro``` approach already in the plugin, with the purpose of having a dedicated command being to automatically turn on the right flags and options for PacBio data rather than relying on the user to do so. There is a downside in the repetition of much of the code between the different ```denoise-[technology]``` commands. **References** 1. Preprint: [High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution](https://www.biorxiv.org/content/early/2018/08/15/392332).

For now, you would have to process your data directly with dada2 using R.

Colin