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lecture_notes:05-24-2010

Our slug DNA is disappearing very quickly. Burn after reading? Convert illumina into something newbler can read.

trim9.goodlength.hist

C is preferable to C++ even although both C and C++ would could be used as long as you are careful.

aligner.py = python module for global and local alignment, used in “find-dna-differences”

find-dna-differences good for finding snips and indels between two assemblies. Outputs bed along with some other formats. Can express snips and indels in “differences” format: sequence:location:sequence

differences2stitcher kstitcher- stitches contigs together

stitcher format: @name comment +contigname -contigname … -(+contig17 -contig18) … 15*N … 12*(-contig8)…

expr1 < expr2 > expr3 means “in expr1 replace the unique expr2 with expr3”

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lecture_notes/05-24-2010.txt · Last modified: 2010/06/05 10:43 by jstjohn