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contributors:team_4_page [2015/05/11 08:49] emfeal [Running ABySS] |
contributors:team_4_page [2015/05/11 09:01] emfeal [Running ABySS] |
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$ABYSSRUN np=10 k=21 name=ecoli in='/campusdata/BME235/programs/abyss-1.5.2/JARED/test-data/reads1.fastq /campusdata/BME235/programs/abyss-1.5.2/JARED/test-data/reads2.fastq' | $ABYSSRUN np=10 k=21 name=ecoli in='/campusdata/BME235/programs/abyss-1.5.2/JARED/test-data/reads1.fastq /campusdata/BME235/programs/abyss-1.5.2/JARED/test-data/reads2.fastq' | ||
</code> | </code> | ||
- | Note that the parallel version of ABySS requires two things in particular: **(1)** the use of a parallel environment which can be selected using a qsub option. The parallel environment option in the script above: | + | Note that the parallel version of ABySS requires two things in particular: |
+ | * **(1)** The use of a parallel environment which can be selected using a qsub option. | ||
+ | * **(2)** The //np// option of abyss-pe. The number of processes here must reflect the number included in the parallel environment option. | ||
+ | The parallel environment option in the script above: | ||
<code> | <code> | ||
#$ -pe mpi 10 | #$ -pe mpi 10 | ||
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qconf -spl | qconf -spl | ||
</code> | </code> | ||
- | **(2)** the //np// option of abyss-pe. The number of processes here must reflect the number included in the parallel environment option. | ||
abyss-pe is a driver script implemented as a Makefile. Any option of make may be used with abyss-pe. Particularly useful options are: | abyss-pe is a driver script implemented as a Makefile. Any option of make may be used with abyss-pe. Particularly useful options are: | ||
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* konnector: fill the gaps between paired-end reads by building a Bloom filter de Bruijn graph and searching for paths between paired-end reads within the graph | * konnector: fill the gaps between paired-end reads by building a Bloom filter de Bruijn graph and searching for paths between paired-end reads within the graph | ||
* abyss-bloom: construct reusable bloom filter files for input to Konnector | * abyss-bloom: construct reusable bloom filter files for input to Konnector | ||
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=====ABySS pipeline===== | =====ABySS pipeline===== | ||