Importing fastq sequences that were previously transformed from ab1 files (Sanger Sequencing)

I have extracted the 16S rRNA from single cultured bacteria and then performed Sanger sequencing for identification purposes (Ihad both forward and reverse sequences for each one.). Therefore, I had ab1 files. After following the suggestion made by @Nicholas_Bokulich in a past question, I have converted the ab1 files to fastq using tracy in a conda environment. However, I am struggling to upload these sequences as QIIME2 artifact to continue with the pipeline suggested by @Nicholas_Bokulich in that forum as follows:

  1. Use q2-quality-filter to filter these reads, dereplicate with q2-vsearch.
  2. Use the classification method of your choice in q2-feature-classifier to taxonomically classify your sequences.
  3. Use the q2-phylogeny plugin to align your sequences and build a phylogeny.

I already had written the fastq manifest as suggested in the qiime2docs. How should I write the code for importing these types of fastq files into QIIME2? Which -- type and --input-format are these fastq files? I have tried --type 'SampleData[Sequences]'. However, I am not sure about the Phred type. Thanks!


It sounds like you have found the importing tutorial but if not, here it is :slightly_smiling_face:

I think you are pretty close, you want your type to be 'SampleData[PairedEndSequencesWithQuality]' and your format to (probably) be PairedEndFastqManifestPhred33V2. Generally any newish data uses a PHRED offset of 33, if not you will get an out of range error and then simply try with 64 instead.

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Many thanks for your reply and your help. It worked as you said with Phred33V2!


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