Banana Slug Genomics

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=====Ray Assembler=====
  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===

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>
mpirun -np 25 -x LD_LIBRARY_PATH=/scratch/jstjohn/lib -machinefile machinefile /scratch/jstjohn/Ray-0.0.7/Ray -p /scratch/galt/bananaSlug/slug_1.fastq /scratch/galt/bananaSlug/slug_2.fastq -s /scratch/galt/bananaSlug/GCLL8Y406.fastq -s /scratch/galt/bananaSlug/GAZ7HUX02.fastq -s /scratch/galt/bananaSlug/GAZ7HUX03.fastq -s /scratch/galt/bananaSlug/GAZ7HUX04.fastq -a SLUG.amos -o slugRay1.fa
**************************************************
This program comes with ABSOLUTELY NO WARRANTY.
This is free software, and you are welcome to redistribute it
under certain conditions; see "gpl-3.0.txt" for details.
**************************************************

Ray Copyright (C) 2010  Sébastien Boisvert, Jacques Corbeil, François Laviolette
http://denovoassembler.sf.net/

AssemblyEngine: Ray 0.0.7
NumberOfRanks: 25
MPILibrary: Open-MPI 1.4.1
OperatingSystem: Linux

LoadPairedEndReads
 Left sequences: /scratch/galt/bananaSlug/slug_1.fastq
 Right sequences: /scratch/galt/bananaSlug/slug_2.fastq
 Average length: auto
 Standard deviation: auto

LoadSingleEndReads
 Sequences: /scratch/galt/bananaSlug/GCLL8Y406.fastq

LoadSingleEndReads
 Sequences: /scratch/galt/bananaSlug/GAZ7HUX02.fastq

LoadSingleEndReads
 Sequences: /scratch/galt/bananaSlug/GAZ7HUX03.fastq

LoadSingleEndReads
 Sequences: /scratch/galt/bananaSlug/GAZ7HUX04.fastq

Preparing AMOS file SLUG.amos
Loading /scratch/galt/bananaSlug/slug_1.fastq

</code>
Banana Slug Genomics

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