Quality Control & Normalization


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