Genome Assembly
Genome assembly is the process of putting together your reads, short-reads, long-reads or both, into long contiguous sequences (contigs). Many different approaches and tools exist to assemble genomes. Assembling long-read data such as PacBio and Oxford Nanopore, into contigs, however, has been challenging for common 2nd generation assemblers due in parts to the high error rates of 3rd generation sequencing technologies. In the last years an increasing number of assemblers and assembly pipelines has been released that are specifically designed for long-read assemblies, e.g., Canu, Flye, Shasta, and miniasm. Furthermoer, several 2nd generation assemblers have been adapted to long-reads and hybrid-assemblies of short- and long reads, such as Spades.
In this tutorial you will use three different assemblers/assembly pipelines, Flye, Shasta and minimap2-miniasm, and compare the results.
1. What is the best assembler to use?
The answer to this question is something like "It depends.". Different assemblers will perform differently for different genomes. Factors such as genome size, repetitiveness, GC content and others can all influence the performance of the assemblers. Best practice is to run multiple assemblers, compare the results and then decide yourself which one to use.
2. When is my assembly done?
Currently, the answer to this question is Never.. As an example: the Human Genome si the best studied genome in the world with thousands of individuals sequenced and millions (billions?) of dollars spent. Still, up to 20% of the Human Genome remains unassembled despite recent advances. This does not mean you can never finish you project. It means your assembly is done when it can answer the questions you want to ask!