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Forum: Open Genomics Engine Project 04-29-2013, 01:56 PM
Replies: 14
Views: 35,791
Posted By adaptivegenome
It has been a year since I posted that message...

It has been a year since I posted that message and since then we decided against developing a GUI. We have functionality that allows you to plug-in external tools into OpenGE (bpipe style) and this...
Forum: General 04-28-2013, 05:11 AM
Replies: 23
Views: 106,586
Posted By adaptivegenome
Hey guys, for those of you are not fans of the...

Hey guys, for those of you are not fans of the citation metric for impact (we are at 9 citations to date) you should check out our Altmetric stats:
...
Forum: Bioinformatics 04-25-2013, 10:46 AM
Replies: 94
Views: 133,200
Posted By adaptivegenome
GCAT is using Bowtie2 and not Bowtie1. Also you...

GCAT is using Bowtie2 and not Bowtie1. Also you can choose what tools are compared or add your own.

You don't even need to use GCAT. I mentioned it because I did not want to make a claim of...
Forum: Bioinformatics 04-25-2013, 09:30 AM
Replies: 94
Views: 133,200
Posted By adaptivegenome
I think that BWA-MEM outperforms both BWA and...

I think that BWA-MEM outperforms both BWA and BWA-SW. You can check out some of the comparisons we have done on gcat (www.bioplanet.com/gcat) and I am sure others here probably have tried out BWA-MEM...
Forum: Bioinformatics 04-15-2013, 09:04 AM
Replies: 14
Views: 4,079
Posted By adaptivegenome
Another great quote from Heng :)

Another great quote from Heng :)
Forum: Bioinformatics 04-15-2013, 07:11 AM
Replies: 14
Views: 4,079
Posted By adaptivegenome
GCAT actually uses DWGSIM, but you are right...

GCAT actually uses DWGSIM, but you are right about the assumptions. GCAT also includes real data for variant calling benchmarks but I think you are right, we should try some other simulators.

We...
Forum: Ion Torrent 04-15-2013, 07:07 AM
Replies: 70
Views: 16,967
Posted By adaptivegenome
Haha! Well good for them! I wonder what happens...

Haha! Well good for them! I wonder what happens to Rothberg & Co.
Forum: Bioinformatics 04-14-2013, 09:08 AM
Replies: 94
Views: 133,200
Posted By adaptivegenome
Here I started a new thread since we have sort of...

Here I started a new thread since we have sort of highjacked this one...

http://seqanswers.com/forums/showthread.php?p=101688#post101688
Forum: Bioinformatics 04-14-2013, 09:05 AM
Replies: 14
Views: 4,079
Posted By adaptivegenome
New way to compare mappers and variant callers

Guys,

I'm starting a new thread for GCAT which is a completely free and collaborative way to compare genome analysis pipelines:

Http://www.bioplanet.com/gcat

You can link to specific...
Forum: Bioinformatics 04-14-2013, 09:00 AM
Replies: 94
Views: 133,200
Posted By adaptivegenome
I would be interested in hearing what suggestions...

I would be interested in hearing what suggestions Heng might have for better metrics. GCAT is awesome but we need to think of more ways to evaluate pipelines...
Forum: General 04-12-2013, 08:45 AM
Replies: 8
Views: 98,502
Posted By adaptivegenome
I would love to know this fits or does not fit...

I would love to know this fits or does not fit within standards for NGS, but we recently unveiled a new online tool with datasets, metrics, and comparison of major NGS pipeline tools. The whole...
Forum: Bioinformatics 03-26-2013, 07:33 PM
Replies: 0
Views: 927
Posted By adaptivegenome
help finding indels, etc. in dbSNP database!

I am grabbing the from the NCBI FTP the dbSNP dataset and I have the files by chromosome that list genome location for the variant but I can't tell if it is SNP, indel, MNP, etc.

Has anyone tried...
Forum: Bioinformatics 03-12-2013, 09:03 PM
Replies: 5
Views: 1,497
Posted By adaptivegenome
Yes, and of course there are other factors that...

Yes, and of course there are other factors that affect indel recall as well (like gap penalty and extension penalty, etc.)...
Forum: General 03-12-2013, 08:54 PM
Replies: 23
Views: 106,586
Posted By adaptivegenome
THank you to everyone that cited the SEQanswers...

THank you to everyone that cited the SEQanswers paper in 2012. According to Google Scholar, the all knowing source of citation info ;) it seems that the paper has already been cited 6 times.
...
Forum: Bioinformatics 03-12-2013, 08:51 PM
Replies: 5
Views: 1,497
Posted By adaptivegenome
No its a good question. If you have a read of...

No its a good question. If you have a read of fixed length and it spans an insertion then you have less sequence that can be used to map the read to the reference.
Forum: Bioinformatics 03-12-2013, 08:47 PM
Replies: 1
Views: 625
Posted By adaptivegenome
anyone going to Bio-IT

I wonder how many SEQanswers community members are going to attend Bio-IT next month? Are there enough members going that we should do a SEQanswers meet up?
Forum: Ion Torrent 03-12-2013, 08:43 PM
Replies: 9
Views: 5,054
Posted By adaptivegenome
Would love to know how the data compares to Ion...

Would love to know how the data compares to Ion Torrent with respect to error/bias.
Forum: Bioinformatics 03-12-2013, 08:42 PM
Replies: 5
Views: 1,497
Posted By adaptivegenome
It common to see a deletion bias with the...

It common to see a deletion bias with the reference. Insertions are harder to map.
Forum: Industry Jobs! 02-06-2013, 08:59 AM
Replies: 0
Views: 3,227
Posted By adaptivegenome
GPU/bioinformatics programmer

http://careers.nvidia.com/pljb/nvidia/nvidiaemployment/applicant/jobClick.jsp?count=1&id=8314

CUDA SOFTWARE ENGINEER - BIOINFORMATICS LIBRARIES #1563619

As a CUDA Software Engineer for...
Forum: Introductions 02-06-2013, 08:56 AM
Replies: 1
Views: 560
Posted By adaptivegenome
Welcome to SEQanswers!

Welcome to SEQanswers!
Forum: General 01-27-2013, 05:49 AM
Replies: 23
Views: 106,586
Posted By adaptivegenome
You can certainly cite the thread ID that is...

You can certainly cite the thread ID that is found in the URL along with the manuscript. Not sure about a single post.

Thanks for wanting to cite our paper!
Forum: Bioinformatics 12-12-2012, 05:40 AM
Replies: 6
Views: 2,904
Posted By adaptivegenome
I saw that. Have you used it? I wonder how it...

I saw that. Have you used it? I wonder how it differs from what 23andMe or SNpedia offers. Does not seem to have much in the way of analysis tools.
Forum: Bioinformatics 12-11-2012, 05:54 PM
Replies: 6
Views: 2,904
Posted By adaptivegenome
I would too but there would be have to something...

I would too but there would be have to something to encourage people to do that. 23andMe already aggregates user data and makes it available to researchers. The key is to identify new ways to gain...
Forum: Bioinformatics 12-11-2012, 04:43 PM
Replies: 6
Views: 2,904
Posted By adaptivegenome
Open source tools for 23andMe data

With the crazy cheap price of 23andMe's chip I wonder what tools we can build to play around with the data. They do a good job of annotating common variants and tracing ancestry. But their data can...
Forum: Bioinformatics 12-05-2012, 06:03 PM
Replies: 5
Views: 1,689
Posted By adaptivegenome
Mapping quality is valuable for variant calling....

Mapping quality is valuable for variant calling. If the quality score does not correspond to accuracy of alignment, this is a big problem I think.
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