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--- archive:bioinformatic_tools:ray [2010/05/19 23:36]
jstjohn created
+++ archive:bioinformatic_tools:ray [2010/05/20 21:17]
jstjohn
@@ Line 2: / Line 2: @@
   wget from ray site
   compiled normally
+See the [[http://denovoassembler.sourceforge.net/|ray wiki]] for further documentation and usage examples.
+====Pog Assembly====
+===Assembly 1===
+===Assembly 2===
-====Assembly 1====
+To generate a fresh machinefile, and execute ray over that machinefile parallelizing over nodes first and slots second:
+<code>
+/campus/BME235/bin/genMach >machinefile
+/campus/BME235/bin/mpirun -machinefile machinefile -x PATH=/campus/BME235/bin:$PATH  -loadbalance --bynode  -np 32 Ray \
+  -s /campusdata/BME235/data/Pog/454_run/sff/FUIPDCZ01.sff \
+  -s /campusdata/BME235/data/Pog/454_run/sff/FUIPDCZ02.sff \
+  -s /campusdata/BME235/data/Pog/sanger/PogSanger.fa \
+  -s /campusdata/BME235/data/Pog/sanger/sequences-3-19-2010.fa \
+  -s /campusdata/BME235/data/Pog/sanger/sequences-3-2-2010.fa \
+  -o slugRay2.fa
+</code>
+Resulting assembly:
+<code>
+2508055 bases (0 N's 2508055 real 2508055 upper 0 lower) in 1392 sequences in 1 files
+Total size: mean 1801.8 sd 1627.0 min 124 (contig-480007) max 12656 (contig-1280008) media
+n 1347
+N count: mean 0.0 sd 0.0
+U count: mean 1801.8 sd 1627.0
+L count: mean 0.0 sd 0.0
+%0.00 masked total, %0.00 masked real
+</code>
+====Slug Assembly====
+===Assembly 1===
 On kolossus:
 <code>

Banana Slug Genomics