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Thread | Thread Starter | Forum | Replies | Last Post |
ERANGE and other packages for RNAseq analysis | warrenemmett | RNA Sequencing | 10 | 10-19-2020 04:53 AM |
Software packages capable of aligning roughly 9000 bp | josecolquitt | Bioinformatics | 4 | 05-18-2010 05:17 AM |
DNAnexus free account: next-gen sequence analysis in the cloud | DNAnexus | Vendor Forum | 0 | 04-27-2010 11:46 PM |
Sequence Analysis Software Developer | Cofactor Genomics | Industry Jobs! | 0 | 01-27-2010 10:02 AM |
Companies offering next gen sequence analysis services | gavin.oliver | Bioinformatics | 8 | 01-12-2010 05:27 AM |
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#141 | |
wiki wiki
Location: Cambridge, England Join Date: Jul 2008
Posts: 266
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Seems that this is exactly the kind of content that a wiki is designed for (not that forums aren't good for what they do! ;-) <asside>Someone should really integrate a decent form system with MediaWiki.</asside> http://en.wikipedia.org/wiki/Next-generation_sequencing Cheers, Dan. |
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#142 |
Senior Member
Location: Oakland, California Join Date: Feb 2008
Posts: 236
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I can check if my hosting will allow one to be installed - for the moment, I'm not even close to using up my bandwidth. Albeit, the domain name doesn't have much to do with next gen sequencing, but maybe someone with a snazzier domain can use a CNAME pointer to pretty it up.
Anthony
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The more you know, the more you know you don't know. —Aristotle |
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#143 |
Senior Member
Location: Oakland, California Join Date: Feb 2008
Posts: 236
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Sorry for the double post - I'm obviously not awake enough this morning. This seems like the perfect application for a Google Knol. (A panel of experts maintaining a single page, wiki stye.)
If anyone is up to it, I'll set it up, and then I can add people who are interested in helping to maintain it. Anthony
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The more you know, the more you know you don't know. —Aristotle |
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#144 |
Member
Location: Sydney, Australia Join Date: Jan 2008
Posts: 83
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I am aware of three 2ndGS software lists out there:
Heng Li keeps one here. There is a 2ndGS list tacked onto an alignment software page on Wikipedia. Unfortunately this page doesn't really suit our purposes considering it is software for alignment only. Someone at the Netherlands Bioinformatics Centre maintains one. This list started of with mostly the seqanswers forum post (I can spy my own writing) but it has been much better maintained and expanded considerably over the last year. Ideally the data should be in table format with columns for sequencing platform support, OS support, read lengths, capabilities, features, memory footprint, links to the journal article, artistic license, etc. Also, in agreement with previous comments a number of administrators is preferable. Perhaps volunteers could maintain their favourite patch of next-gen turf? |
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#145 |
Nils Homer
Location: Boston, MA, USA Join Date: Nov 2008
Posts: 1,285
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I think this should do for wikipedia:
http://en.wikipedia.org/wiki/List_of...ence_Alignment Look under "Short-Read_Sequence_Alignment". Please contribute to this list if anyone gets the chance. |
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#146 | |
wiki wiki
Location: Cambridge, England Join Date: Jul 2008
Posts: 266
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SMW is basically a wiki database system. |
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#147 |
Member
Location: Sydney, Australia Join Date: Jan 2008
Posts: 83
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#148 |
wiki wiki
Location: Cambridge, England Join Date: Jul 2008
Posts: 266
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I've been using SMW quite a bit - I can probably get something 'beta' quikly going under 'ngs.referata.com' (or where ever). Then we can start to develop in the wiki style.
Hopefully Wikipedia will start to run SMW some time soon. In the mean time we can develop under SMW and try to manually keep up with the relevant lists on Wikipedia. |
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#149 |
Junior Member
Location: Amsterdam, NL Join Date: Feb 2009
Posts: 5
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"Someone at the Netherlands Bioinformatics Centre maintains one." Hey, that's us!
"This list started of with mostly the seqanswers forum post (I can spy my own writing)" That's right, I started searching to add to the list (I didn't start it), and then found this forum. I thought I had struck gold, but then it turned out the seqanswers-list was the basis... Haha, never thought anyone other then us would use our list. Good to read. Yeah, the list has been left alone pretty much lately and I have a lot more info to put in there, but I didn't see the necessity until now. I'll try to update soon and let you people know. Cheers! |
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#150 |
Member
Location: LONDON, UNITED KINGDOM Join Date: Jan 2009
Posts: 44
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How about those softwares for data analysis, like CASAVA, SAMtools and FindFeatures?
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#151 |
Member
Location: northern hemisphere Join Date: Mar 2008
Posts: 50
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Swift: Primary Data Analysis for the Illumina Solexa Sequencing Platform
Open source primary data analysis pipeline. Image analysis/basecalling. Paper here: http://bioinformatics.oxfordjournals...bstract/btp383 Download it here: http://swiftng.sourceforge.net Abstract: Motivation: Primary data analysis methods are of critical importance in second generation DNA sequencing. Improved methods have the potential to increase yield and reduce the error rates. [Openly documented analysis tools enable the user to understand the primary data, this is important for the optimisation and validity of their scientific work.] Results: In this paper we describe Swift, a new tool for performing primary data analysis on the Illumina Solexa Sequencing Platform. Swift is the first tool, outside of the vendors own software, which completes the full analysis process, from raw images through to base-calls. As such it provides an alternative to, and independent validation of, the vendor supplied tool. Our results show that Swift is able to increase yield by 13.8%, at comparable error rate. Availability and Implementation: Swift is implemented in C++ and supported under Linux. It is supplied under an open source license (LGPL3), allowing researchers to build upon the platform. Swift is available from http://swiftng.sourceforge.net. |
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#152 | |
--Site Admin--
Location: SF Bay Area, CA, USA Join Date: Oct 2007
Posts: 1,358
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I'm working on this as we speak...I have SMW and MediaWiki running on my private mirror of this site, however I'm hindered by the fact that I'm not savvy enough with SMW to implement it well. If you guys (and anyone else...) is up for helping out populate, etc, it's pretty straightforward to activate a SMW-ified mediawiki installation here. The main thing I think we need to move forward, is a data structure for these software packages. Maybe I'll just put it up tonight and let you guys loose. |
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#153 |
wiki wiki
Location: Cambridge, England Join Date: Jul 2008
Posts: 266
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Hi ECO,
I've been thinking about this a lot since it got suggested. One of the things that worries me is the proliferation of sites and locations where such a list should (or could) be maintained. I didn't realise until I looked that the NBIC list IS a wiki (1), and therefore, taking the well maintained content from that site and putting it into 'yet another wiki' seems like a potential waste of time (duplication of effort, splitting of an existing user base, etc., etc.). However, I think it *could* be useful to apply SMW, because of its powerful query and browsing features. Now, because I have a connection to Bioinformatics.Org, I'd like to try to implement the list there, but it should somehow be tied to both NBIC *and* Wikipedia (somehow) and other sites. Also, I don't want to just stomp all over your efforts to set up a SMW install here. So basically, my first hurdle was where and not what. I still haven't resolved that issue. Looking to the next step, deciding a data structure is important to do early on. SMW emulates a database in the wiki, but it isn't trivial to modify the structure of the wiki-DB once it has been set up. My plan was to simply follow what was being done at the NBIC (i.e. get their table of data into an equivalent wiki-DB table). For learning, first, I'd recommend you read the guidelines here: http://www.mediawiki.org/wiki/Extension:Semantic_Forms I'll see if I can get a dummy system up and running on Bioinformatics.Org (if only for demonstration purposes). Actually my guess is that the NBIC will install SMW in short order once we demonstrate what can be done with it (the user base there makes it a good choice for a permanent location for such a list...). So the question is, how to integrate our effort? |
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#154 |
Member
Location: Udine (Italy) Join Date: Jan 2009
Posts: 50
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The problem about the NBIC cite is that there is no organization. I think that for the community a wiki well organize is something really important. In the NBIC you can see in random order viewers, assembler of long and short reads, reference assemblers.
I think that the most important think is not only provide links to literature or to the web sites where tool can be downloaded but also provide personal experiences. I give an example: In every list allpaths is cited as a a good de novo assembler but it seems impossible to use it. Some thing for shorty, it can be compiled but do to the lack of documentation is not possible use it... |
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#155 |
wiki wiki
Location: Cambridge, England Join Date: Jul 2008
Posts: 266
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Well, I got something up and running as quickly as I could here:
http://www.bioinformatics.org/wiki/S...ta/Sandbox_ngs Note, the category (or 'class') I used for the pages is "Sandbox ngs", because this is still 'work in development', i.e. it's in the 'sandbox'). Basically I dumped the table from the NBIC wiki: https://wiki.nbic.nl/index.php/High_...ncing#Software into the Semantic MediaWiki at Bioinformatics.Org using the 'Data Transfer' extension and the 'Semantic Forms' extension (and the page above is generated by the Semantic Drilldown extension). Try clicking on a page to see the data, currently crudely formatted in a wiki table for the package in question. For example: http://www.bioinformatics.org/wiki/MUMmer Notice the new 'edit with form' tab that Semantic Forms provides. For example: http://www.bioinformatics.org/w/inde...ction=formedit Finally, as a very brief example of the querying capabilities of the SMW, I have recreated the table seen on the NBCI page here: http://www.bioinformatics.org/wiki/Sandbox/Software Wherever the data ends up, I hope the above can be useful for demonstrating the features of SMW. Clearly we do need a better data model for the software, and integrating user experiences, feedback and rating needs to be carefully done. We don't want to duplicate the function of this forum, for example. HTH, Dan. Last edited by dan; 07-20-2009 at 03:49 AM. Reason: fixed the very first link |
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#156 |
Junior Member
Location: Maryland Join Date: Jul 2009
Posts: 1
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Awesome work!!!!
Has anyone heard/used AYB algorithm on Illumina GA? If you do use it would you give some contrast comparisons with other algorithms. I don't seem to find information about AYB on the web, if you know of any URL please pass it on, I truly appreciate the help. |
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#157 | |
Member
Location: Germany Join Date: May 2008
Posts: 79
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Quick question: is it possible to add multiple tags? I'm just asking because many packages offer different functionalities (e.g. mapping to reference, de novo assembly, SNP detection) which is difficult to catch in only one tag. Some categories are a bit vague at the moment, e.g., the difference between "Assembly" and "Assembly (de-novo)" is eluding me, but this is something which could be quickly resolved. Regards, B. |
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#158 | |
wiki wiki
Location: Cambridge, England Join Date: Jul 2008
Posts: 266
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Second point, I just copied the data from the table at the NBIC: https://wiki.nbic.nl/index.php/High_...ncing#Software (let me know if you see any differences ;-) We can rationalize this much better using the autocompletion and controlled vocabularies that the SMW system supports. Dan. |
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#159 |
Junior Member
Location: USA Join Date: Jun 2009
Posts: 5
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#160 |
Junior Member
Location: Germany Join Date: Jul 2009
Posts: 4
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Thanks for the nice post Sci_quy! It´s very helpful.
Unfortunately, there is no software package for Tag-Seq (Tag-Profiling/Illumina) Data listed/available. Does anybody know, whether there exist specific packages and if this is the case which one is best to use? Or is it possible to use standard programs for RNA-Seq (like ERANGE)? I´ve read about an in-house perl script. Does anybody have an equivalent? Is it possible to test it? Thanks a lot. |
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