Resources to learn genome assembly workflow for small genomes (like viruses)

Rezaeir · 08-16-2020, 08:43 AM

I have sequencing data of a few samples of a `DNA genome virus`. I'd like to learn `de novo assembly` of the `short reads`, making scaffolds from it, and then `counting the abundance` of each strain in the data. I heard about `SPAdes` as a good choice for these kinds of very short genomes. and also `BBmap` for statistics related to contigs.

I am a complete newbie in everything related to de novo assembly. So, I wonder if you could recommend some good `courses/tutorials/papers` for learning all the steps, including units, special vocabularies, analysis steps, and everything else.

I have some experience with analyzing `RNA-seq` and also `small RNA-seq` data. I learned these two using free online resources, however, it is very hard to find even one full workflow post/paper on `genome assembly`.

Note: I know that I should read the documentation on `SPAdes` and `BBmap` and I will. However, I'd like to first get to a good idea of what are the steps, test it on some sample data, and then go through learning different tools. So, it is like saying that I need to learn RNA-seq analysis not read a particular `aligner` documentation.

cross-posted in bioinformatics.stackexchange and biostars.

SeoSpiderCat · 03-13-2021, 03:30 AM

Thanks for the helpful resource! I recently wrote a research paper on the genome and studied this article in detail - https://www.topwritersreview.com/blo...esearch-paper/ . This article helped me better understand how to write a quality essay, and I got the highest score.

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08-16-2020, 08:43 AM	#1
Rezaeir Junior Member Location: Tehran Join Date: Aug 2020 Posts: 1	Resources to learn genome assembly workflow for small genomes (like viruses) I have sequencing data of a few samples of a `DNA genome virus`. I'd like to learn `de novo assembly` of the `short reads`, making scaffolds from it, and then `counting the abundance` of each strain in the data. I heard about `SPAdes` as a good choice for these kinds of very short genomes. and also `BBmap` for statistics related to contigs. I am a complete newbie in everything related to de novo assembly. So, I wonder if you could recommend some good `courses/tutorials/papers` for learning all the steps, including units, special vocabularies, analysis steps, and everything else. I have some experience with analyzing `RNA-seq` and also `small RNA-seq` data. I learned these two using free online resources, however, it is very hard to find even one full workflow post/paper on `genome assembly`. *Note: I know that I should read the documentation on `SPAdes` and `BBmap` and I will. However, I'd like to first get to a good idea of what are the steps, test it on some sample data, and then go through learning different tools. So, it is like saying that I need to learn RNA-seq analysis not read a particular `aligner*` documentation. cross-posted in bioinformatics.stackexchange and biostars.

03-13-2021, 03:30 AM	#2
SeoSpiderCat Member Location: Aricona, Phoenix Join Date: Oct 2020 Posts: 16	Thanks for the helpful resource! I recently wrote a research paper on the genome and studied this article in detail - https://www.topwritersreview.com/blo...esearch-paper/ . This article helped me better understand how to write a quality essay, and I got the highest score. Last edited by SeoSpiderCat; 03-17-2021 at 03:52 AM.