Notes on illumina sequencing

• How Illumina sequencing works: https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2017/Day1/Session4-seqIntro.html

• Matreyek lab dual indexing description Succinct description of how Illumina sequencing works for different flow cell designs, with a specific focus on custom sequencing and index read primer.

• Amplicon sequencing detailed information from Norwegian Sequencing Center Describes the minimum sequence requirements for custom paired end sequencing design. Note the extra sequence necessary at the P5 end for paired-end sequencing.

• In NextSeq, Read 1 and Read 2 primers are pooled before loading. The two index primers (i5 and i7) are pooled before loading.

• The first base of Read 1 sequencing should not be a G or a T since both of these are dark.