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--- archive:bioinformatic_tools:gs_de_novo_assembler [2010/04/20 14:17]
karplus Added warning about non-serial conting numbering, added -noace
+++ archive:bioinformatic_tools:gs_de_novo_assembler [2010/04/24 15:48]
karplus Put -rst 0 back in, with explanation
@@ Line 44: / Line 44: @@
 == De novo assembly ==
-The standard commands for de novo assembly are to create a new directory, and in that directory create a Makefile that includes a target to execute the following commands:
+The standard approach for de novo assembly is to create a new directory, and in that directory create a Makefile that includes a target to execute the following commands:
 <code>
 newAssembly .
 addRun . /campusdata/BME235/data/Pog/454_run/sff/FUIPDCZ01.sff
 addRun . /campusdata/BME235/data/Pog/454_run/sff/FUIPDCZ02.sff
-runProject -e 50 -noace -rst 0 .
+runProject -e 50 -nobig -rst 0 .
 </code>
 Of course, different sff files will be used on different runs.
+The "-e" value is the expected coverage.  For the Pog 454 data, that should be about 60.  For the banana-slug data, it is very much smaller (0.05?).
+The -nobig parameter suppresses the generation of big output files.
+The -rst 0 parameter (repeat score threshold) says that a read should be labeled uniquely mapped if its best hit scores >0 more than the next best (the default value is 12, which means that a lot of hits get labeled as repeats, even though they can distinguish between similar repeat regions).
 A Makefile that illustrates the use of the SunGrid to avoid running on the head node is shown in /campusdata/BME235/assemblies/Pog/newbler-assembly2/Makefile
@@ Line 67: / Line 73: @@
 addRun . /campusdata/BME235/data/Pog/454_run/sff/FUIPDCZ01.sff
 addRun . /campusdata/BME235/data/Pog/454_run/sff/FUIPDCZ02.sff
-runProject -e 50 -noace -rst 0 .
+runProject -e 50 -nobig -rst 0 .
 </code>

Banana Slug Genomics

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