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archive:bioinformatic_tools:allpaths [2010/04/06 15:27]
jstjohn
archive:bioinformatic_tools:allpaths [2015/07/28 06:22] (current)
ceisenhart ↷ Page moved from bioinformatic_tools:allpaths to archive:bioinformatic_tools:allpaths
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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_2.pdf|allpathsv3_manual}}.
 +
 +====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 which I assume means shared memory, so it may not work on our cluster. Maybe it would be useful to run on small portions of our data though?
 +
 ====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 3.1) 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 3.2) 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. ​
  
 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// 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//
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 Perhaps our data will not behave nicely with this algorithm? Also they didn't say whether or not they combine the reads from those three sources, or somehow analyze them separately and merge them at some point. Perhaps reading more into their documentation or publications will answer some of these questions. --- //​[[jstjohn@soe.ucsc.edu|John St. John]] 2010/04/05 17:50// Perhaps our data will not behave nicely with this algorithm? Also they didn't say whether or not they combine the reads from those three sources, or somehow analyze them separately and merge them at some point. Perhaps reading more into their documentation or publications will answer some of these questions. --- //​[[jstjohn@soe.ucsc.edu|John St. John]] 2010/04/05 17:50//
 +===== Installation =====
 +Installed statically on isla.cse.ucsc.edu and transferred over.
 +
 +Installed with boost_1.38 and gcc version 4.4. 
 +
 +The installed the binaries here:
 +  /​projects/​lowelab/​users/​jstjohn/​allpaths/​bin
 +
 +and then I ziped them and transfered them via scp over to campusrocks. ​
 +
 +To compile static I ran configure with "​CXXFLAGS=-static"​. ​
 +
 +They also installed graphviz on the computer which is necessary to view some of the output, although I am pretty sure this isn't a pre-requisite to compile the program as the configure script never bugged me about specifying the graphviz source and/or binary. ​
 +
 +
  
 ===== References ===== ===== References =====
 <​refnotes>​notes-separator:​ none</​refnotes>​ <​refnotes>​notes-separator:​ none</​refnotes>​
 ~~REFNOTES cite~~ ~~REFNOTES cite~~
archive/bioinformatic_tools/allpaths.1270567642.txt.gz · Last modified: 2010/04/06 15:27 by jstjohn