Software packages for next gen sequence analysis

[wuhoucdc]

Thanks Sci_guy pasted such a great resource!

[sci_guy]

Cheers

Thanks Sci_guy pasted such a great resource!

Also big ups to ECO, Dan, et al. for the Wiki. I've been on the back foot lately in maintaining this list; too busy in the lab. An abstract deadline for the AACR Cancer Epigenetics conference next year to meet

[ohomann]

Hello everyone,

I was wondering if you would mind adding MochiView, my hybrid genome browser and motif visualization/analysis software, to this list.

Here is a link to the section of the MochiView website with three quick demo videos.

MochiView is particularly useful to anyone interested in identifying/analyzing/managing motifs (multiple motif libraries are available on the MochiView website for import into the software). In addition, members of various labs around UCSF are using the software to visualize/analyze Chip-Chip, Chip-Seq, and RNA-Seq data.

Here are a few more details for those interested:

• MochiView is desktop Java software with an integrated database
• MochiView has a rich interface for configuring/saving plot layouts
• The browser has smooth panning/zooming and a very useful data browsing function
• MochiView contains a large number of motif utilities, including motif comparison, motif position distribution, motif ROC plots, several motif scoring functions, ability to rapidly export motif scoring of location sets or promoters to spreadsheet, etc.
• MochiView also contains some Location/Data Set manipulation utilities (e.g. set operations and filters)
• The website contains a tutorial for download that can familiarize you with many of the basic features
• MochiView will write and publish your paper for you. OK, that feature isn't quite ready yet

One thing MochiView does NOT do is "peak-calling" for Chip-Chip or Chip-Seq. MochiView leaves this to the many existing solutions and is more appropriate for downstream visualization and analysis.

Thanks for your time,
Oliver Homann
Johnson Laboratory
UCSF

[dan]

Hey Oliver,

I've been working developing the 'wiki arm' of the SEQempire (called SEQwiki) so that it can be used as a browsable / query-able archive of "Software packages for next gen sequence analysis" [1]. The content was seeded from a table on the NBIC wiki [2], which was originally seeded from this list!

It's still work in progress, but the best 'first impression' is probably here:

http://seqwiki.com/wiki/Special:BrowseData

(Lots of packages still need data adding.)

Since setting it up there have been quite a few packages added, mostly by KRobinson but also many others [3]. Please have a go at adding MochiView to the wiki, and let us know how you got on (any good / bad features, etc.).

Cheers,
Dan.

[1] http://seqwiki.com
[2] http://wiki.nbic.nl/index.php/High_t...ncing#Software
[3] http://seqanswers.com/w/index.php?ti...s=30&limit=500 - I still haven't got the query interface working to get proper reports on contributions.


P.S. Perhaps ECO should archive/sticky this thread, create a forum for the wiki and somehow (sticky thread?) let people know to start using the wiki?

[ohomann]

Hey Oliver,
Please have a go at adding MochiView to the wiki, and let us know how you got on (any good / bad features, etc.).

Hi Dan,

Thanks, I actually found the wiki and added MochiView just after posting to this thread. FWIW, the upload image option doesn't seem to work (it tells me that I don't have a proper extension on my file).

Thanks for the great resource!

[ECO]

P.S. Perhaps ECO should archive/sticky this thread, create a forum for the wiki and somehow (sticky thread?) let people know to start using the wiki?

I've been considering losing this thread for a while, mainly because any replies in this thread end up emailing about 50% of the members who have either subscribed or posted in the thread (Hi everyone! ).

The second improvement would be to link all these packages to their respective wiki pages.

As a side note, I don't want anyone to get wedded to the new domain seqwiki.com, as the seamless cross-site authentication with the forum accounts does not work. Seqwiki.com is fine for viewing, but wiki.seqanswers.com will be the only one that is editable for a while. (They share the same database). Let's keep this discussion in another thread, perhaps in that "Wiki Development" forum I keep forgetting to set up.

Hi Dan,

Thanks, I actually found the wiki and added MochiView just after posting to this thread. FWIW, the upload image option doesn't seem to work (it tells me that I don't have a proper extension on my file).

Thanks for the great resource!

Hmm...perhaps Dan could fix this.

[dan]

I still haven't got the query interface working to get proper reports on contributions.

Here is is finally!

The result is pretty awesome! Thanks everyone for taking part!

(I'll break this down to remove 'robot' edits, which is the reason why I currently have so many)

SELECT
  user_name, user_editcount 
FROM 
  user 
ORDER BY 
  user_editcount DESC 
;

user_name	user_editcount
Dan		478
Krobison 	229
Andreas.sjodin 	209
ECO		56
Cariaso 	12
Taoliu		5
Maubp		5
Apfejes 	4
Nilshomer 	4
Simonandrews 	4
Weese		4
Wjeck		3
Yxi		3
Ohomann 	3
BaCh		3
Dfornika 	3
HAA		3
Jkbonfield 	2
Ben Langmead 	2
Kevleb		2
Joa ds		2
Dawe		2
Balajis 	1
Lparsons 	1
Jonathan 	1
AlwaysSNP 	1
Mmartin 	1
Lh3		1

[Y.Y. LEUNG]

What is the best Align/Assemble tool?

Hi All,

I am a new user of NGS softwares. Thanks a lot for providing such a list. Are there any updates on the information provided?

with so many tools (e.g. in the ALign/assemble field), do anyone has any idea on which tool are the best for use (in terms of ease of usage and computation time required)?

Thanks a lot.

Fanny Leung

[dan]

Hi All,

I am a new user of NGS softwares. Thanks a lot for providing such a list. Are there any updates on the information provided?

with so many tools (e.g. in the ALign/assemble field), do anyone has any idea on which tool are the best for use (in terms of ease of usage and computation time required)?

I know the feeling!

I'm going to start a 'standard operating procedures' (SOP) section on the wiki to document case studies based on various requirements.

Basically the answer to your question depends on what data you have, what you are trying to do with your data, and what OS you are familiar with. If you can supply those details, I'm sure there will be several suggestions of how to proceed.

[wuhoucdc]

Hi all,

Who have the time to summarize the programs that can be used call SV such as large rearrangement, deletion, amplication among NGS? Thanks.

Wuhoucdc

[ECO]

Hi all,

Who have the time to summarize the programs that can be used call SV such as large rearrangement, deletion, amplication among NGS? Thanks.

Wuhoucdc

You are more than welcome to start annotating the software packages in our wiki: http://wiki.seqanswers.com. I believe Dan is working on a set of instructions for new wiki users.

Thanks!

[wuhoucdc]

Thanks ECO for your kind suggestions.

Wuhoucdc

[Y.Y. LEUNG]

Seems that most of the softwares are available in Linux environment.

Are there any softwares recommended for use in Windows for RNA-seq or targeted sequencing projects? the data are obtained from Solexa, 454 and SoLID.

Thanks for your help.

[nilshomer]

Seems that most of the softwares are available in Linux environment.

Are there any softwares recommended for use in Windows for RNA-seq or targeted sequencing projects? the data are obtained from Solexa, 454 and SoLID.

Thanks for your help.

I am tempted to push you toward cygwin.

[apfejes]

Depends what you're trying to do - I've used Vancouver Short Read Analysis Package/FindPeaks (my own software) for RNA-Seq (alternative exon expression) and had good luck - I don't use it in windows, myself, but java is cross-platform and I know people have successfully used in that environment.