Number of polishing iterations in Flye assembly and Pseudogene count

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Hello,

I was following the tutorial of Hands-on: Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data) / Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data) / Assembly

When I submitted the assembly file from MinION data to NCBI, they reported more than 30% pseudogenes.

I have a question about the number of polishing iterations in Flye Galaxy Version 2.9.3. I’ve used 3 iterations, but I’m wondering if it’s okay to increase the number during assembly and if so, to what extent can I increase it?

Do you have any other suggestions to improve my assembly?

Additionally, I am interested in learning about any recommended tools for checking pseudogene and frameshift counts in the final assembly files.

Thanks in advance! :smiling_face:

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Hi @l.r.l.s.k

This tutorial has a good overview of post-assembly quality control steps. Might be worth a review, especially if NCBI detected annotation features that you didn’t realize were present before the submission. → Hands-on: Genome Assembly Quality Control / Genome Assembly Quality Control / Assembly. For predicting annotation, see these tutorials. → Genome Annotation / Tutorial List

For more … I’m not qualified to offer more advice for this species but we do have microbial community members that have experience. :slight_smile:

I’m going to cross post your question over to the Gitter/Matrix chats linked at the top of the GTN site to see if that can get things started. They may reply here to there, and feel free to join the chat. You're invited to talk on Matrix

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Hi Jennaj,

Thank you very much for the valuable information and help.

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