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- | ====== ABySS ====== | + | ======Team 4 | ABySS ====== |
**A**ssembly **By** **S**hort **S**equences - a //de novo//, parallel, paired-end sequence assembler | **A**ssembly **By** **S**hort **S**equences - a //de novo//, parallel, paired-end sequence assembler | ||
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=====ABySS overview===== | =====ABySS overview===== | ||
- | ABySS is published by Canada's Michael Smith Genome Sciences Centre, and was the first //de novo// assembler for large genomes recommended bu Illumina in [[http://www.illumina.com/Documents/products/technotes/technote_denovo_assembly_ecoli.pdf|this technical note]] when using only their data. | + | ABySS is published by Canada's Michael Smith Genome Sciences Centre, and was the first //de novo// assembler for large genomes recommended bu Illumina in [[http://www.illumina.com/Documents/products/technotes/technote_denovo_assembly_ecoli.pdf|this technical note]] when using only their data. The ABySS team are active members on [[https://www.biostars.org/t/Abyss/|BioStars]] where they recommend all technical questions be asked. |
[[http://www.bcgsc.ca/platform/bioinfo/software/abyss | ABySS main site]] | [[http://www.bcgsc.ca/platform/bioinfo/software/abyss | ABySS main site]] | ||
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[[https://github.com/bcgsc/abyss| ABySS manual and source code]] | [[https://github.com/bcgsc/abyss| ABySS manual and source code]] | ||
+ | =====Installing ABySS===== | ||
+ | |||
+ | ABySS source code was downloaded from Github | ||
+ | <code> | ||
+ | % lftpget https://github.com/bcgsc/abyss/archive/master.zip | ||
+ | </code> | ||
+ | ABySS needs to be configured with it's dependencies | ||
+ | <code> | ||
+ | % ./autogen.sh | ||
+ | % ./configure --prefix=/campusdata/BME235\ | ||
+ | % --enable-maxk=96\ #must be a multiple of 32 | ||
+ | % --enable-dependency-tracking\ | ||
+ | % --with-boost=/campusdata/BME235/include/boost\ | ||
+ | % --with-mpi=/campusdata/BME235/include\ | ||
+ | % CC=gcc-4.9.2 CXX=g++-4.9.2\ | ||
+ | % CPPFLAGS=-I/campusdata/BME235/include/sparsehash | ||
+ | </code> | ||
+ | Then ABySS can be installed via the makefile | ||
+ | <code> | ||
+ | % make | ||
+ | % make install | ||
+ | </code> | ||
=====ABySS parameters===== | =====ABySS parameters===== | ||
- | Parameters of the driver script, abyss-pe | + | Parameters of the driver script, abyss-pe, and their [default value] |
* a: maximum number of branches of a bubble [2] | * a: maximum number of branches of a bubble [2] |