Banana Slug Genomics

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====== Brief overview of goals and data input characteristics ======
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:
==== Sanger capillary ====
  * ~800bp reads[(cite:wikisanger>http://en.wikipedia.org/wiki/Microfluidic_Sanger_sequencing)].
  * Q (quality value) ~30
  * ~$1/read, expensive because primers must be attached to each read.
==== 454 ====
  * ~400bp reads[(cite:wiki454>http://en.wikipedia.org/wiki/454_Life_Sciences)].
  * Pyrosequencing
  * Q ~20
  * $5000/run/1M reads, no downscaling (numbers approximate).
==== SoLiD ====
  * 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).
==== Illumina ====
  * 2x50, 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.
==== Ion Torrent ====

==== Pac Bio ====
  * Very long, single molecule reads (~10K)
  * High error rates (~5%)
  * Useful when mapping to a reference.
===== References =====
<refnotes>notes-separator: none</refnotes>
~~REFNOTES cite~~

Banana Slug Genomics

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