Recently, I had to understand the basics of genome assembly. Genome assembly refers to the process of 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.
In a genome sequencing project, the DNA of the target organism is broken up into millions of small pieces and read on a sequencing machine. These “reads” vary from 20 to 1000 nucleotide base pairs (bp) in length depending on the sequencing method used. Typically, for Illumina type short read sequencing, reads of length 36 - 150 bp are produced.
The goal of a sequence assembler is to produce long contiguous pieces of sequence (contigs) from these reads. The contigs are sometimes then ordered and oriented in relation to one another to form scaffolds.
Genome assembling glossary
- Genome — The genetic material of an organism. The genome incorporates a full set of chromosomes. A chromosome carries the genetic information for each cell. Each chromosome contains many genes, which are in turn made up of DNA and protein combined as chromatin.
- DNA — Deoxyribonucleic acid is the chemical compound that contains the instructions needed to develop and direct the activities of nearly all living organisms.
- Base — DNA is made of four chemical units, called nucleotide bases. The bases are adenine (A), thymine (T), guanine (G), and cytosine (C).
- Base pairs (bp) — In the DNA double helix, bases come in pairs. A always pairs with T and C always pairs with a G.
- Read — A small sequence of base pairs. Short reads contain hundreds of bps. Long reads contain thousands of bps.
- Contigs — Long contiguous pieces of sequence. Generating contigs from smaller reads is the goal of genome assemblers.
- De Bruijn graph — A compact representation based on short words (k-mers) that is ideal for high coverage, very short read (25–50 bp) data sets.
- FastQ — A text-based file format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores.
Genome assemblers software
There are several genome assembler software packages that differ in Programming Language (PL), size of reads (short of long) and support for error correction. A useful comparison of genome assemblers can be found here: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0169662.
| Genome Assembler | PL | Reads | Error correction |
|---|---|---|---|
| SPAdes | C++ | Short and Long | Yes |
| Velvet | C | Short | Yes |
| SOAPdenovo2 | C | Short | Yes |
| Megahit | C++ | Short | Yes |
| Raven | C++ | Long | No |
Resources
I found the following youtube videos very helpful.
Video series by Dr. Loren Launen:
Video-lecture by Jared Simpson (Ontario Institute for Cancer Research):