R packages for genome assembly in R

Question

[choi.yisoo.hi]

Hi, I have some questions about assembly. I am a really beginner so probably my questions are look like stupid questions. I know.;((((

1. Is there any package for assembly(especially de novo)?

2. What is different alignment(mapping) and assembly?

And if you know the way to do assembly please tell me.

Thank you.

Answer 1

[lakhujanivijay]

Since you say that you are "really beginner" , I would suggest spare some time reading about genome assembly before you really get your hands dirty with actually doing it. Here are some fantastic resources I would suggest

De novo Genome Assembly for Illumina Data

De novo genome assembly [Happy Belly Bioinformatics]

Ten steps to get started in Genome Assembly and Annotation

A field guide to whole-genome sequencing, assembly and annotation

Do it yourself guide to genome assembly

Is there any package for assembly(especially de novo)?

Reading through these articles, you will soon realize that you actually don't need an R package for assembly purpose (I would be surprised if such packages do exist), rather, there are several open source/commercial/paid/free, C/python/PERL based programs/software/packages that are actually used/developed in industry/academia.

What is different alignment(mapping) and assembly?

If you just google "assembly meaning", you will see this:

google says - assembly is the action of gathering together as a group for a common purpose.

In case of genome assembly, the "common purpose" is taking a large number of short DNA sequences and putting them back together to create a representation of the original chromosomes from which the DNA originated (source). Most commonly, a denovo assembly is performed when you do not have a well defined genome for your organism; for e.g. when you are working with non-model organisms. However, it varies on case-by-case basis.

Whereas, in case of mapping we want to answer the question about the reads (short DNA stretches) - "where did it (read) come from?". So you sequence your sample and get multiple reads and try to create a "map" of the genome by mapping the reads on to a well defined genome already present.

[choi.yisoo.hi]

Thank you very much.

I was so confused.

Your answer is very helpful.

[lakhujanivijay]

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