archive:bioinformatic_tools:allpaths
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archive:bioinformatic_tools:allpaths [2010/04/06 15:24] jstjohn |
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| 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 3.1) 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 3.1) 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. | ||
| - | In class I mentioned that a fellow student, Amie, had a lot of trouble with assembling via Euler. Actually that program was ALLPATHS, but when she used it at the beginning of last quarter it was still in version 1.0. According to Broad version 1.0 was only expected to work on test data (although Amie couldn't even get that working)[(cite:broad)]. Since then they have come out with two major revisions and one minor revision, and they claim that this version works on real data, so I think it is definitely worth a shot. --- //[[jstjohn@soe.ucsc.edu|John St. John]] 2010/04/06 08:21// | + | In class I mentioned that a fellow student, Amie, had a lot of trouble with assembling via Euler. Actually that program was ALLPATHS, but when she used it at the beginning of last quarter it was still in version 1.0. According to Broad version 1.0 was only expected to work on test data[(cite:broad)] (although Amie couldn't even get that working). Since then they have come out with two major revisions and one minor revision, and they claim that this version works on real data, so I think it is definitely worth a shot. --- //[[jstjohn@soe.ucsc.edu|John St. John]] 2010/04/06 08:21// |
| ===Expected Data Quality=== | ===Expected Data Quality=== | ||
archive/bioinformatic_tools/allpaths.txt · Last modified: 2015/07/28 06:22 by ceisenhart
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