I am a newbie in this field, can anyone give me a list on the name of the current available software for Ion Proton data analysis?References recommendation is also welcome.Thank you guys so much!
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
If you are looking for the official Ion Torrent Suite software then as far as I know there is no way to get it unless you have a machine. (http://www.lifetechnologies.com/us/e...-software.html) There is a cloud version (but that is not free either: https://torrentsuite.lifetechnologies.com/)
Life Tech has the "Ion reporter software" that is cloud based. I am not sure if that is free but the information is available at the link above (look in the navigation bar on the left).
Otherwise the output from an Ion Proton machine is regular fastq-format data files. You can pretty much use any NGS software that can handle this data for analysis. One thing to keep in mind is the quality scores from Ion runs are not completely equivalent to normal phred scores.Last edited by GenoMax; 11-08-2013, 05:57 AM.
-
Hi there GenoMax,
In fact, Torrent Suite software (and a few other packages) is open source and is freely available via our github repository:
https://github.com/iontorrent
As mentioned on the Torrent Suite page, starting with our freely available virtual machine is another option. But these options are largely intended for developers, rather than people looking for an end user solution.
At the present time, Ion Reporter is available freely at the following location:
The next version of Ion Reporter, which has a number of exciting updates and improvements, is due next month.
Originally posted by GenoMax View PostIf you are looking for the official Ion Torrent Suite software then as far as I know there is no way to get it unless you have a machine. (http://www.lifetechnologies.com/us/e...-software.html) There is a cloud version (but that is not free either: https://torrentsuite.lifetechnologies.com/)
Life Tech has the "Ion reporter software" that is cloud based. I am not sure if that is free but the information is available at the link above (look in the navigation bar on the left).
Otherwise the output from an Ion Proton machine is regular fastq-format data files. You can pretty much use any NGS software that can handle this data for analysis. One thing to keep in mind is the quality scores from Ion runs are not completely equivalent to normal phred scores.
Comment
-
Thanks for those links. I will have to look into getting the software.
Curiously when this topic had come up locally no one from Life Tech said anything about the availability of the software on github (which was the origin of my comment above).
Is it possible to grab a folder of raw data from the proton/PGM and analyze it offline using a separate TS install?
Comment
-
Sorry, we might have missed the earlier post. Please do consider Ion Community for those kinds of requests as well - there are team members monitoring the various spaces who are dedicated to responding. We do value the great resource that SEQanswers is as well and try to respond where we can here as well!
Yes, that is correct. It is easiest starting from so-called WELLS files. The guidance in the Torrent Suite Administration Guide found on Ion Community should provide helpful information. Outside of that, the best course is to speak with a local Field Bioinformatics Scientist.
Originally posted by GenoMax View PostThanks for those links. I will have to look into getting the software.
Curiously when this topic had come up locally no one from Life Tech said anything about the availability of the software on github (which was the origin of my comment above).
Is it possible to grab a folder of raw data from the proton/PGM and analyze it offline using a separate TS install?
Comment
-
Can someone offers me a guidance of Torrent suite?
I read the Readme, but I cannot find the guidance on how to use this software apart from the guidance of installing this software. Where can I get the manual? Thanks
Originally posted by IonTorrent View PostHi there GenoMax,
In fact, Torrent Suite software (and a few other packages) is open source and is freely available via our github repository:
https://github.com/iontorrent
As mentioned on the Torrent Suite page, starting with our freely available virtual machine is another option. But these options are largely intended for developers, rather than people looking for an end user solution.
At the present time, Ion Reporter is available freely at the following location:
The next version of Ion Reporter, which has a number of exciting updates and improvements, is due next month.
Comment
-
Originally posted by cindylanzao View PostI read the Readme, but I cannot find the guidance on how to use this software apart from the guidance of installing this software. Where can I get the manual? Thanks
Comment
Latest Articles
Collapse
-
by seqadmin
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
Channel: Articles
04-04-2024, 04:25 PM -
-
by seqadmin
Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...-
Channel: Articles
03-22-2024, 06:39 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
24 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
25 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
||
Started by seqadmin, 04-10-2024, 09:21 AM
|
0 responses
21 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 09:21 AM
|
||
Started by seqadmin, 04-04-2024, 09:00 AM
|
0 responses
52 views
0 likes
|
Last Post
by seqadmin
04-04-2024, 09:00 AM
|
Comment