archive:bioinformatic_tools:gs_de_novo_assembler
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archive:bioinformatic_tools:gs_de_novo_assembler [2010/04/16 01:37] karplus bug notice, installed wrong version |
archive:bioinformatic_tools:gs_de_novo_assembler [2010/04/24 15:36] karplus replaced -noace by -nobig and added explanations |
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| * stopRun | * stopRun | ||
| - | (but I haven't tested them yet --- //[[karplus@soe.ucsc.edu|Kevin Karplus]] 2010/04/15 16:02//) | + | Installed and being tested |
| - | BUG: I installed the old version...I'll have to try again with the 2.3 version. --- //[[karplus@soe.ucsc.edu|Kevin Karplus]] 2010/04/15 18:36// | + | |
| == De novo assembly == | == 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> | <code> | ||
| newAssembly . | newAssembly . | ||
| addRun . /campusdata/BME235/data/Pog/454_run/sff/FUIPDCZ01.sff | addRun . /campusdata/BME235/data/Pog/454_run/sff/FUIPDCZ01.sff | ||
| addRun . /campusdata/BME235/data/Pog/454_run/sff/FUIPDCZ02.sff | addRun . /campusdata/BME235/data/Pog/454_run/sff/FUIPDCZ02.sff | ||
| - | runProject -e 50 . | + | runProject -e 50 -nobig . |
| </code> | </code> | ||
| Of course, different sff files will be used on different runs. | 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. | ||
| + | |||
| + | 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 | ||
| + | |||
| + | Note: earlier versions of Newbler provided serially numbered contigs, but version 2.3 seems to skip numbers rather arbitrarily, so that the range of the numbers is larger than the size of the set of contigs. Look at the counts (in assembly/454NewblerMetrics.txt) or run a program to count the contigs, rather than relying on the largest contig number. | ||
| == Mapping to existing genome == | == Mapping to existing genome == | ||
| Line 64: | Line 71: | ||
| addRun . /campusdata/BME235/data/Pog/454_run/sff/FUIPDCZ01.sff | addRun . /campusdata/BME235/data/Pog/454_run/sff/FUIPDCZ01.sff | ||
| addRun . /campusdata/BME235/data/Pog/454_run/sff/FUIPDCZ02.sff | addRun . /campusdata/BME235/data/Pog/454_run/sff/FUIPDCZ02.sff | ||
| - | runProject -e 50 . | + | runProject -e 50 -nobig . |
| </code> | </code> | ||
archive/bioinformatic_tools/gs_de_novo_assembler.txt · Last modified: 2015/07/28 06:23 by ceisenhart
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