archive:bioinformatic_tools:allpaths
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archive:bioinformatic_tools:allpaths [2010/04/07 07:54] jstjohn |
archive:bioinformatic_tools:allpaths [2010/04/07 09:23] jstjohn |
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| ===== ALLPATHS ===== | ===== ALLPATHS ===== | ||
| + | Attached is the Allpaths3 version 1.0 documentation converted from .docx format to .pdf. You can download this file by clicking the following link: {{:bioinformatic_tools:allpathsv3_manual_r1.0.pdf|allpathsv3_manual_r1.0.pdf}}. | ||
| + | ====Potential Pitfalls==== | ||
| + | Designed to work with 100+ bp paired end reads from a *minimum of one short and one long set of libraries. Also the program expects 40X coverage from each of those libraries! Additionally they say it requires a minimum of 32Gb of ram, but for a full sized mammalian genome they recommend 512Gb of ram!! I assume they mean shared memory here so this program may be a no go. I am building the program but stopping short of installing it due to these limitations. | ||
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| ====High Level Overview==== | ====High Level Overview==== | ||
| ALLPATHS is the most recent (as of this writing) tool developed by the broad institute to assemble shotgun sequences[(cite:broad>http://www.broadinstitute.org/science/programs/genome-biology/computational-rd/computational-research-and-development)]. The broad institute claims that version 3 of the program can assemble up to mammalian sized genomes if the reads are at least 100+ base pairs[(cite:broad)]. Version 3 (currently 3.2) of the program may be downloaded from [[ftp://ftp.broad.mit.edu/pub/crd/ALLPATHS/Release-3-0/|here]] and that folder also contains some documentation on how to use the program. Also the program ships with test data that you can assemble. | ALLPATHS is the most recent (as of this writing) tool developed by the broad institute to assemble shotgun sequences[(cite:broad>http://www.broadinstitute.org/science/programs/genome-biology/computational-rd/computational-research-and-development)]. The broad institute claims that version 3 of the program can assemble up to mammalian sized genomes if the reads are at least 100+ base pairs[(cite:broad)]. Version 3 (currently 3.2) of the program may be downloaded from [[ftp://ftp.broad.mit.edu/pub/crd/ALLPATHS/Release-3-0/|here]] and that folder also contains some documentation on how to use the program. Also the program ships with test data that you can assemble. | ||
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| Boost successfully installed. Now installing allpaths. Configure successful and currently building. --- //[[jstjohn@soe.ucsc.edu|John St. John]] 2010/04/07 00:53// | Boost successfully installed. Now installing allpaths. Configure successful and currently building. --- //[[jstjohn@soe.ucsc.edu|John St. John]] 2010/04/07 00:53// | ||
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| + | Build unsuccessfull: | ||
| + | ./ParallelVecUtilities.h: In function 'void ParallelSort(vec<T>&)':\\ | ||
| + | ./ParallelVecUtilities.h:27: error: '__gnu_parallel' has not been declared\\ | ||
| + | ./ParallelVecUtilities.h: In function 'void ParallelSort(vec<T>&, StrictWeakOrdering)':\\ | ||
| + | ./ParallelVecUtilities.h:35: error: '__gnu_parallel' has not been declared\\ | ||
| + | ./ParallelVecUtilities.h: In function 'void ParallelReverseSort(vec<T>&)':\\ | ||
| + | ./ParallelVecUtilities.h:42: error: '__gnu_parallel' has not been declared\\ | ||
| + | ./ParallelVecUtilities.h: In function 'void ParallelReverseSort(vec<T>&, StrictWeakOrdering)':\\ | ||
| + | ./ParallelVecUtilities.h:50: error: '__gnu_parallel' has not been declared\\ | ||
| + | ./ParallelVecUtilities.h: In function 'void ParallelWhatPermutation(const V&, vec<T3>&, C, bool)':\\ | ||
| + | ./ParallelVecUtilities.h:316: error: '__gnu_parallel' has not been declared | ||
| ===== References ===== | ===== References ===== | ||
| <refnotes>notes-separator: none</refnotes> | <refnotes>notes-separator: none</refnotes> | ||
| ~~REFNOTES cite~~ | ~~REFNOTES cite~~ | ||
archive/bioinformatic_tools/allpaths.txt · Last modified: 2015/07/28 06:22 by ceisenhart
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