Assembly of reads using genome reference

1

What programs are available for assembly of genome to reference using mapped reads???

2

Hi @Jon_Colman

Glad to see you are making progress.

So.. in general, there are three ways to “assemble” reads. Some of these are not true full assemblies but rather descriptive comparisons versus the baseline assembly. We have tutorials for all of these.

  1. Full assembly. The reference is mostly used to filter the reads to consider for the assembly process rather than directly guiding it then later on used to refine an assembly. The read types (DNA versus RNA) matter when choosing the tool/protocol.

    • Search the tool panel with the keyword spades to see one option for a popular tool suite.
    • Then flye is an example for a different class of reads (single cell).
    • For refinement, a tool like pilon is an example.
    • (Then, tutorials are linked at the bottom of tool forms for these listed examples.)
    • Or, see here directly. → Assembly / Tutorial List
    • There any many tool choices – see the tool panel under Assembly to review. Most have a publication that you can review, and those will be cited by other publications from the scientists who have used to that tool to generate public data. Your reference assembly probably also has a publication, and reviewing what they original did could be informative (not just the tool choice, but for organism-specific assembly challenges!).

  2. Psuedo-assembly. This is a type of scaffolding against the reference assembly. It is commonly used to examine splicing differences or presence/absence of features for expression analysis projects. The data here is RNA.

  3. Variants. This is looking at “SNPs” (single nucleotide polymorphisms) but in practical applications those can involve one or more nucleotides (MNPs, multiple nucleotide) and even larger rearrangements. Importantly for you, this type of protocol is commonly used to identify and classify organism strains in public health projects, and we have examples of that in the tutorials. The data is usually DNA, but RNA is possible.

Then there are hybrids of all of these! But maybe this helps to get you oriented? :slight_smile: