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--- lecture_notes:03-30-2011 [2011/03/30 23:32]
eyliaw [SoLiD]
+++ lecture_notes:03-30-2011 [2011/04/01 19:20] (current)
svohr [Coverage] slight corrections
@@ Line 20: / Line 20: @@
   * $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 ====
+  * 2x100 base pairs
+  * ~50,000 to 5,000,000 reads depending on Sequencing Chip [(cite:ionTorrent>http://www.iontorrent.com/technology-how-does-it-perform/)].
+  * Ion semiconductor sequencing. No optics or modified bases are required.
 ==== Pac Bio ====
+  * Very long, single molecule reads (~10K)
+  * High error rates (~5%)
+  * Useful when mapping to a reference.
+===== Coverage =====
+We briefly discussed how much sequence data would be required to assemble the genome. First, we considered the probability of seeing a particular base ''i'' in a single read ''j''.
+  P( seeing base i in read j ) = L/G
+where ''L'' is the read length and ''G'' is the total size of the genome. If we have ''R'' reads, then
+  P( never seeing base i ) = (1 - L/G)^R
+We can multiply ''L/G'' by ''R/R'' to get ''((L*R) / G) / R'' or ''C / R'' where ''C'' is our coverage of the genome. We take the limit of this as
+''R'' goes to infinity:
+  lim n->inf (1 - C/R)^R = e^-C
+Thus we can expect to miss ''G*e^-C'' bases.
+We cannot assemble an entire chromosome if we are missing bases. However, we can construct contiguous stretches of bases or //contigs// and later
+assemble them into //scaffolds// using other information, such as long distance physical maps.
 ===== References =====
 <refnotes>notes-separator: none</refnotes>
 ~~REFNOTES cite~~

Banana Slug Genomics

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