Introduction to Metagenomics
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Genomics looks at the whole genome content of an organism
Metagenomes contain multiple organisms within one sample unlike genomic samples.
In metagenomes the organisms present are not usually present in the same abundance - except for mock communities.
We can identify the organisms present in a sample using either amplicon sequencing or whole metagenome sequencing. Amplicon sequencing is cheaper and quicker, however it also limits the amount of downstream analysis that can be done with the data.
Metagenomes can differ in their levels of complexity and this is determined by how many organisms are in the metagenome.
Difference platforms allow us to perform different analyses. The suitability depends on the question you are asking.
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Logging onto the Cloud
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Assessing Read Quality, Trimming and Filtering
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Quality encodings vary across sequencing platforms.
It is important to know the quality of our data to be able to make decisions in the subsequent steps.
Data cleaning is essential at the beginning of metagenomics workflows.
Due to differences in the sequencing technology Nanopore data must be handled differently.
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Metagenome Assembly
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Assembly merges raw reads into contigs.
Flye can be used as a metagenomic assembler.
Certain statistics can be used to describe the quality of an assembly.
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