raw Illumina data

What is a read?

A read is a sequence that is generated by the NGS process. Each cluster on the flow cell represents one fragment from the library and will give rise to one sequence. This sequence is called a read.

A read is much smaller than the fragment it originates from. Typically, fragments are 100-900 bp long while reads are 40-150 bp. A read comes from one of the ends of the fragment.

In single end sequencing each fragment will generate one read, in paired end sequencing, each fragment will generate two reads, one from each end of the fragment.

What is a base?

In each cycle of the sequencing one nucleotide is added to the PCR products in a cluster and the identity of this nucleotide (A, C, G or T) is determined by the base calling software. A base is therefore one nucleotide in a read.