Does Qiime2 support straight forward analysis for Sanger sequencing results?

Hi, again a beginner question!

I extracted DNA from single cultured bacteria and Sanger sequenced. Now, I have ab1 files. I used to manually trim and align sequences in Geneious software and use MEGA, BLAST search etc… But, wondering if there is a more efficient way to do taxonomy assignment and build phylogenetic trees in Qiime2.

It looks like I need to convert all ab1 files to FASTA first to import data in Qiime2 environment. But, I got lost what to do afterwards because all tutorials are described based on next-generation sequencing. I really appreciate having information where I should find to learn entire protocols from trim/alignment to taxonomy assignment and phylogenetic tree for “Sanger Sequencing” results.

Thank you.

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Sure!

  1. convert ab1 to fasta outside of QIIME 2
  2. import fasta to QIIME 2 as a FeatureData[Sequence] artifact (see the importing tutorial on qiime2.org for details)
  3. use the classification method of your choice in q2-feature-classifier to taxonomically classify your sequences.
  4. use the q2-phylogeny plugin to align your sequences and build a phylogeny.

You will probably still need to manually trim before converting to fasta, but it might also be possible to convert ab1 to fastq and use q2-quality-filter to filter these reads, dereplicate with q2-vsearch, and then proceed to step 2 above.

Let us know what you find!

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