contributors:team_4_page
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contributors:team_4_page [2015/05/07 23:24] JaredC |
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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] | ||
| Line 83: | Line 105: | ||
| * abyss-scaffold: scaffold contigs using distance estimates | * abyss-scaffold: scaffold contigs using distance estimates | ||
| * abyss-todot: convert graph formats and merge graphs | * abyss-todot: convert graph formats and merge graphs | ||
| + | |||
| + | =====ABySS pipeline===== | ||
| + | |||
| + | |||
| + | {{ :bioinformatic_tools:abysspipeline.png?nolink |}} | ||
contributors/team_4_page.txt · Last modified: 2015/07/18 20:52 by 92.247.181.31
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