Software packages for next gen sequence analysis

[apfejes]

I have a fairly complete set of RNA-Seq tools in the Vancouver Short Read Analysis Package, although they've never been published.

[apfejes]

spam? The hidden link is pretty sneaky.

[ECO]

spam? The hidden link is pretty sneaky.

Yup, I got 'em in moments, but I'm considering adding moderation of posts to this thread so everyone doesn't get emailed when that happens. :/

[apfejes]

Thanks ECO,

It's so hard to stay one step ahead of the spammers. I probably should have refreshed before replying. Sorry to those who are getting excessive emails. :/

Anthony

[sci_guy]

Hi thread followers,

I've spent most of the last year in the wet lab implementing a new epigenomics method for SOLiD and Illumina so I've had no time to update the table at the start of this thread. I'm moving onto the 'dry' phase now and are hunting around for software to assist in my analysis. Anyway, I took this opportunity to update the table. Apologies to those who have PMed me over the last long while asking for their software to be added.

I hope to keep this table a little better maintained, but the amount of software out there is exploding (just like the amount of data and potential applications of 2nd Gen Seq). In light of this I cannot promise the table will be comprehensive for that much longer.

Cheers,
sci_guy

[dan]

I hope to keep this table a little better maintained, but the amount of software out there is exploding (just like the amount of data and potential applications of 2nd Gen Seq). In light of this I cannot promise the table will be comprehensive for that much longer.

Wiki anyone? I'm sure there is a space for this kind of list on Wikipedia (which, incidentally, doesn't even have an article dedicated to NGS) or we could use one of the existing sci-wikis out there (e.g. http://OpenWetWare.Org, http://Bioinformatist.Org, http://MetaDataBase.Org, ... ).


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.

[apfejes]

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

[apfejes]

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

[sci_guy]

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?

[nilshomer]

I think this should do for wikipedia:

http://en.wikipedia.org/wiki/List_of_sequence_alignment_software#Short-Read_Sequence_Alignment

Look under "Short-Read_Sequence_Alignment". Please contribute to this list if anyone gets the chance.

[dan]

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?

Sounds like a job for Semantic MediaWiki - We can register a free SMW site at referata.com and start playing around with ideas.

SMW is basically a wiki database system.

[sci_guy]

Sounds like a job for Semantic MediaWiki - We can register a free SMW site at referata.com and start playing around with ideas.

Sounds good

[dan]

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.

[dePhi]

"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!

[inesdesantiago]

How about those softwares for data analysis, like CASAVA, SAMtools and FindFeatures?