Kevin laid out some of the logistics of the class.

A broad goal: For each chromosome in the slug, we want the full sequence in DNA bases. Since it is unlikely to be completed in the timeframe of one quarter, some smaller goals: build contigs and have an idea of the scaffold to arrange the contigs in.

Inputs: Sequencing data from various machines. Some of the characteristics of these machines/techniques:

• ~800bp reads[1].
• Q (quality value) ~30
• ~$1/read, expensive because primers must be attached to each read.

• ~400bp reads[2].
• Pyrosequencing
• Q ~20
• $5000/run/1M reads, no downscaling (numbers approximate).

• 2x25bp or 1x50bp reads
• Paired end reads: ligation with adapter, cleaves 25bp from adapter using restriction enzyme.
• Potential for double ligation: two unrelated sequences ligating.
• $2000/run/100M reads (numbers approximate).

• 2×50, 2x100bps ?
• Paired end reads
• Potential errors: innies (ligated region not between sequenced regions) or chimeric (sequence passes ligated region)
• Cheaper than SoLiD, 10K Genomes project uses it.