Genbank annotation transfer.
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3.7 years ago

As the Title implies, I am looking for a set of tools (Linux command line only - I don't have a GUI) that can do a whole genome alignment as follows:

I have the NC_045512 reference genbank file for SARS-CoV-2, and I want to align a complete sequence (call it "Seq_A") with it. The output contains either a genbank file of Seq_A, or a gff of the annotations from the reference genbank file. Any suggestions?

genome alignment sequence gene sequencing • 1.5k views
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Have you tried RATT?

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I tried RATT, but for some reason it wasn't working. I haven't spent too much time debugging because I am swamped, but given the suggestion by multiple people, I'll give it another go...

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Please edit the title to make it concise.

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Hi, I was biologist and I'm currently IT dev, I'm working on a tool to do that mostly for bacteria. You can try the whole Prokka tool, or start with Prodigal (from hyattpd) only. And/Or you can send me your files, I'll be pleased to test my app with this kind of data.

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Try out LifeBit they offer a free trial and I've been using them for Whole Genome Sequencing for a Trio analysis. They offer various tools and allow you to pull open source code into the platform to run more pipelines. In my opinion they aren't very expensive either. You can also use docker container, which is a plus.

The tools on lifebit I'd recommend are either Bowtie2 or BWA.

Link for LifeBit is here - https://lifebit.ai/

Please note I am not an affiliate of LifeBit and have nothing to gain from recommending them I just think they are an efficient tool to use especially when dealing with not having a GUI and having to deal with larger files for WGS.

If you have any questions feel free to reach out or comment I'll gladly help.

Also note if you decide to use LifeBit in your Data section where you upload your data make sure you create a project then a project folder and upload the files needing to be used in that project folder not just in the project. This issue caused complications for me as you can't directly move them once uploaded so it was annoying to have to re-upload them.

An alternative but pricey platform would be BaseSpace by Illumina, but they are truly great.

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This is not an answer to the specific question asked in original post and is being moved to a comment.

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3.7 years ago
Joe 21k

I would suggest RATT (as did Genomax), or the more recent tool liftoff from Steven Salzberg's lab.

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