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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 [2010/05/28 22:30]
jstjohn
@@ 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
 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.
+For large genomes you can pass the -large argument to runProject and it will take some time-saving shortcuts.
+<code>
+        ${BIN}/newAssembly .
+        ${BIN}/addRun . ${SFFS_IN}
+        ${BIN}/addRun . ${FA_IN}
+        ${BIN}/runProject -e ${EXPECTED_COVERAGE} -large -rst 0 -noace .
+</code>
 == Mapping to existing genome ==
@@ Line 67: / Line 81: @@
 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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