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Search: Posts Made By: Len Trigg
Forum: Vendor Forum 06-19-2017, 06:35 PM
Replies: 2
Views: 3,499
Posted By Len Trigg
New stable releases are now available which...

New stable releases are now available which include minor improvements and bug fixes.

The first of these is our full analysis suite, RTG Core 3.8.2. The changes in this version are listed below....
Forum: Vendor Forum 06-01-2017, 06:59 PM
Replies: 2
Views: 3,499
Posted By Len Trigg
New stable releases are now available which...

New stable releases are now available which include minor improvements and bug fixes.

The first of these is our full analysis suite, RTG Core 3.8.1. The changes in this version are listed below. ...
Forum: Vendor Forum 05-15-2017, 08:38 PM
Replies: 2
Views: 3,499
Posted By Len Trigg
RTG 3.8: New QC tools / improved machine learning / free simulation tools

Real Time Genomics are pleased to announce the availability of new releases of our full analysis suite, RTG Core, and our utility package, RTG Tools. This release includes new features and...
Forum: Vendor Forum 10-17-2016, 03:08 PM
Replies: 1
Views: 3,092
Posted By Len Trigg
New stable releases are now available which...

New stable releases are now available which include minor improvements and bug fixes.

The first of these is our full analysis suite, RTG Core 3.7.1. The changes in this version are listed below. ...
Forum: Vendor Forum 08-25-2016, 08:28 PM
Replies: 1
Views: 3,092
Posted By Len Trigg
RTG 3.7: Somatic calling improvements / targetted sequencing / variant comparison etc

Real Time Genomics are pleased to announce the availability of new releases of our full analysis suite, RTG Core, and our utility package, RTG Tools. This release includes new features and...
Forum: Vendor Forum 03-13-2016, 06:06 PM
Replies: 2
Views: 2,081
Posted By Len Trigg
New stable releases are now available which...

New stable releases are now available which include minor improvements and bug fixes.

The first of these is our full analysis suite, RTG Core 3.6.1. The changes in this version are listed below....
Forum: Vendor Forum 01-25-2016, 11:05 AM
Replies: 2
Views: 2,081
Posted By Len Trigg
New stable releases are now available which...

New stable releases are now available which include minor improvements and bug fixes.

The first of these is our full analysis suite, RTG Core 3.6.1. The changes in this version are listed below. ...
Forum: Vendor Forum 12-06-2015, 06:50 PM
Replies: 2
Views: 2,081
Posted By Len Trigg
RTG 3.6: Somatic improvements / CGI v2 read support / variant evaluation

Real Time Genomics are pleased to announce the availability of new releases of our full analysis suite, RTG Core (commercial / free for non-commercial use), and our utility package, RTG Tools (BSD...
Forum: Bioinformatics 10-18-2015, 03:36 PM
Replies: 4
Views: 1,937
Posted By Len Trigg
Check the tool that you are using to output your...

Check the tool that you are using to output your brief format above -- I suspect that it is not taking into account the padding base that is added to pure insertions/deletions (in order to prevent an...
Forum: Bioinformatics 10-18-2015, 12:54 PM
Replies: 4
Views: 1,937
Posted By Len Trigg
The positions of the indels are not "wrong", just...

The positions of the indels are not "wrong", just different. For example, the first case, the reference genomic sequence from 13:32893197-32893208 is:
ATTTTTTTTTTA

The Roche version of the...
Forum: Vendor Forum 10-15-2015, 05:33 PM
Replies: 2
Views: 2,021
Posted By Len Trigg
New stable releases are now available which...

New stable releases are now available which include minor improvements and bug fixes.

The first of these is our full analysis suite, RTG Core 3.5.2. The changes in this version are listed below. ...
Forum: Bioinformatics 10-04-2015, 02:53 PM
Replies: 3
Views: 3,417
Posted By Len Trigg
While this post is a little old, it is worth...

While this post is a little old, it is worth noting that the joint Bayesian variant calling of RTG Core (http://realtimegenomics.com/products/rtg-core/) does directly incorporate pedigree information...
Forum: Bioinformatics 10-04-2015, 02:43 PM
Replies: 1
Views: 1,785
Posted By Len Trigg
If you are interested in the algorithms behind...

If you are interested in the algorithms behind indel calling in general, the method used by RTG Core (http://realtimegenomics.com/products/rtg-core/) for indel calling (and complex haplotype calling)...
Forum: Illumina/Solexa 09-24-2015, 07:16 PM
Replies: 3
Views: 1,156
Posted By Len Trigg
"1" represents a haploid call, such as on the...

"1" represents a haploid call, such as on the non-PAR regions of X and Y for a male sample. RTG Core (http://realtimegenomics.com/products/rtg-core/) variant callers also automatically output haploid...
Forum: Vendor Forum 09-07-2015, 02:53 PM
Replies: 2
Views: 2,021
Posted By Len Trigg
New stable releases are now available which...

New stable releases are now available which include minor improvements and bug fixes.

The first of these is our full analysis suite, RTG Core 3.5.1. The changes in this version are listed below. ...
Forum: Vendor Forum 07-16-2015, 01:39 PM
Replies: 2
Views: 2,021
Posted By Len Trigg
RTG 3.5: Somatic calling / metagenomics / variant comparison / BSD Licensing

Real Time Genomics are pleased to announce the availability of new releases of our full analysis suite, RTG Core (commercial / free for non-commercial use), and our utility package, RTG Tools (free...
Forum: Bioinformatics 06-08-2015, 01:23 PM
Replies: 5
Views: 6,372
Posted By Len Trigg
Just noticing your comment about problem with...

Just noticing your comment about problem with indels when using MuTect. You might want to try the RTG somatic caller (part of RTG Core), which uses the same haplotype calling engine as the regular...
Forum: Bioinformatics 05-28-2015, 01:52 PM
Replies: 4
Views: 2,113
Posted By Len Trigg
You should absolutely be using rtg vcfeval to...

You should absolutely be using rtg vcfeval to perform the comparison, as it correctly handles the differences in variant representation that different callers produce. Other comparison tools do not...
Forum: Vendor Forum 05-27-2015, 02:23 PM
Replies: 4
Views: 2,689
Posted By Len Trigg
RTG Core 3.4.5 / RTG Tools 3.4.5

New stable releases are now available which include minor improvements and bug fixes. In particular, those using the somatic caller or vcfeval/rocplot will benefit from updating to the new release. ...
Forum: Bioinformatics 05-13-2015, 12:52 PM
Replies: 16
Views: 2,895
Posted By Len Trigg
Jo, The 1-50bp note is more about the...

Jo,

The 1-50bp note is more about the default RTG mapping settings (you'd have to start adjusting the aligner settings to look for longer indels, at somewhat of a speed penalty). The variant...
Forum: Bioinformatics 05-11-2015, 03:59 PM
Replies: 674
Views: 172,696
Posted By Len Trigg
Brian, Thanks for the reply, that clears...

Brian,

Thanks for the reply, that clears things up nicely! (I agree with you about adjusting the readme.)

Cheers,
Len.
Forum: Bioinformatics 05-11-2015, 02:46 PM
Replies: 674
Views: 172,696
Posted By Len Trigg
Hi Brian, Could you please clarify the...

Hi Brian,

Could you please clarify the license for BBMap? I thought I might try a couple of runs with it for fun, but once I installed it I saw conflicting license information. In the top level of...
Forum: Bioinformatics 05-03-2015, 01:18 PM
Replies: 16
Views: 2,895
Posted By Len Trigg
Hi Jo, You can try the caller from RTG Core,...

Hi Jo,

You can try the caller from RTG Core, which will call the haplotypes over the region as a whole, and includes an allelic depth attribute in the VCF which should include exactly the counts...
Forum: Vendor Forum 04-20-2015, 02:03 PM
Replies: 4
Views: 2,689
Posted By Len Trigg
RTG Core 3.4.4 / RTG Tools 3.4.4

New stable releases are now available which include minor improvements and bug fixes. In particular, heavy users of vcfeval or rocplot will benefit from updating to the new release.

The first of...
Forum: Metagenomics 03-22-2015, 01:25 PM
Replies: 7
Views: 2,160
Posted By Len Trigg
For the pathway analysis you can try RTG mapx and...

For the pathway analysis you can try RTG mapx and then feed the results to Megan. mapx is significantly faster than blastx.

If you want to look at taxonomy-aware composition analysis, perhaps RTG...
Showing results 1 to 25 of 29

 


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