added bibliography, small edits elsewhere#6

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jfass wants to merge 12 commits intovsbuffalo:masterfrom

Commits on Jun 7, 2012

some edits to paper .tex
jfass
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Commits on Jun 13, 2012

finished a round of paper edits - JNF
jfass
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Commits on Jun 29, 2012

fixed naming of original solexa adapters
jfass
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Commits on Jul 11, 2012

minor formula fix - reversing the contaminant / non-contaminant cases of maximum a priori rule application
jfass
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Merge branch 'master' of github.com:jfass/scythe
jfass
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Commits on Aug 21, 2012

added helper script to mine reads for (TruSeq) sample IDs
jfass
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Commits on Aug 22, 2012

Merge pull request #2 from jfass/master
UC Davis Bioinformatics Core
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Commits on Sep 26, 2012

added bib to tex, small edits
jfass
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