Could you please let me know if it is possible to run dada2 in qiime2 for either of sanger or nanopore sequencing or it is only for Illumina sequencing?
Asking for a friend
Cheers
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Hello @MarwaTawfik,
Dada2 was originally designed for illumina reads. There are actions in qiime now for analyzing output from circular consensus sequencing and pyrosequencing in dada2, but not for nanopore or Sanger sequencing.
The issue with nanopore sequencing seems to be the high error rate, and the issue with Sanger sequencing seems to be the low number of sequences one would expect to have.
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Many thanks @colinvwood
Heard of any workflow/package that might be used for either sequencing (sanger and nanopore)?
You might try what is described in this post for Sanger generated sequences, I think this should at least get you started analyzing your data!
As @colinvwood pointed out, Oxford Nanopore sequences have a higher error rate than say Illumina generated short reads, but not only this, they tend to suffer from different types of errors than short read sequencing technologies (see this paper). The QIIME 2 project thus far has focused on amplicon-based analyses, which means that most of our efforts have been directed towards building high quality tools appropriate for short read technologies. With the coming release of a shotgun metagenomics toolkit, we may need to turn more of our attention to tools for working with other sequencing data, but there is no active work being done in this direction yet.
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