Quality Control & Normalization

Metagenomics.wiki

Genome (assembly) QC

Genome quality & annotation tools


→ Coverage depth

How many short reads mapped to a genome sequence?


→ Sample size

How deep do we have to sequence?


→ RPKM calculation

Normalization for comparing gene coverage values


→ Phred score (Q score)

Measure for base quality


→ Giga base pairs

Sequence length in numbers of base pairs


→ GC content

Guanine-cytosine (GC) content of a genome sequence



Shotgun Sequencing QC

Full genome shotgun sequencing


→ Read quality control and trimming

remove low-quality reads and adapter sequences


→ Remove host sequences

 bowtie2 alignment