Software packages for next gen sequence analysis

[todd]

Originally Posted by ECO

I have, but I haven't heard much about their service. I would invite them to come and introduce the community to the service.

Thanks ECO,

Geospiza is a software company in Seattle specializing in automation systems for genetic analysis. We have products (FinchLab and iFinch) to handle both LIMS and analysis needs for Next Gen sequencing. These products are being delivered in novel cost effective ways so that groups do not have build data centers for their new machines.

Many folks know of us from FinchTV. To learn more you can visit our web site . You can also check out our blog FinchTalk, where we give short demos and discuss the issues we see with next generation sequencing.

Please visit, we'd like to hear what you are doing and see if we can help.

Cheers,

Todd
Geospiza, Inc.

[ECO]

I've read in a couple of places that someone has written an ELAND-->GBrowse script that will let you view the assembly in Gbrowse...but I can't find any actual projects.

[ECO]

Originally Posted by todd

Thanks ECO,

Geospiza is a software company in Seattle specializing in automation systems for genetic analysis. We have products (FinchLab and iFinch) to handle both LIMS and analysis needs for Next Gen sequencing. These products are being delivered in novel cost effective ways so that groups do not have build data centers for their new machines.

Many folks know of us from FinchTV. To learn more you can visit our web site . You can also check out our blog FinchTalk, where we give short demos and discuss the issues we see with next generation sequencing.

Please visit, we'd like to hear what you are doing and see if we can help.

Cheers,

Todd
Geospiza, Inc.

Hey Todd, Nice to see you on board! I copied your post to a new thread so more people will see it!

[Chipper]

Originally Posted by ECO

I've read in a couple of places that someone has written an ELAND-->GBrowse script that will let you view the assembly in Gbrowse...but I can't find any actual projects.

Don't know about GBrowse, but what I have found useful is to convert the Eland files to .bed files with the sequences and just upload it to the UCSC GB. Just rc the -strand reads and change positions based on sequence length will make it align at the bp view.

[apfejes]

Originally Posted by bioinfosm

Thanks apfejes
I know of the FindPeaks tool ... the others you mention are available somewhere to download and try?

I am looking to use a few of the short read tools available to see how they perform on the solexa data,. and what tweaks i can learn... but that requires being able to go from their output to something more friendly

next, the visualizations are just a good way to be able to depict data, in case it is feasible

Hey Bioinfosm,

Sorry - they're not publicly available yet, but I'm always looking for beta testers/collaborators. Send me a PM, if you're interested.

[bioinfosm]

Anyone tried that? Converting the MAQ or SHrimp alignment to .ace file format, which can be used in the EagleView tool from Marth Lab?

I was looking for a good way to convert alignments to .ace file format

sm

[tp_a]

does findpeaks only accept eland files? what other files i can run using findpeaks?

[apfejes]

Hi tp_a,

The current version on the web accepts Eland files only, and one type of vulgar format from Exonerate, though I also have a version that will work with BED files.

I'm currently working on FindPeaks 3.2, which should accept several of the extended Eland formats and possibly MAQ, but there's really no reason to limit the types of file it can process. If you want to send me an example file format of whatever file format you're working on (and possibly some documentation on the file type), I'd be very happy to add support for it in FindPeaks.

It usually takes me about 15 minutes to add a new file format, if it's well documented.

Cheers,

Anthony

[tp_a]

thanks anthony for the info. will do for now.

A.

[JKing]

Another couple of tools:

SeqMan Genome Assembler -- an assembler (as opposed to a templated read aligner) of Illumina, 454, and/or Sanger single read and paired end data. Output as .ace assemblies or .sqd SeqMan format. Two algorithms ~ de novo or, when references are used, a hybrid algorithm using a combination templated/de novo approach that eliminates the problem of reads getting thrown out even in especially SNPy areas.

The primary viewing and genome completion tool is SeqMan Pro 8, which now includes SNP filtering options to eliminate noise and/or to only annotate reference SNPs of interest. Annotation support provides information like SNP A causes a.a. change B in codon C of CDS/exon D, as well as cross-annotation of the consensus from the reference sequence for use of the consensus in subsequent steps. The other tool for analysis is ArrayStar, which imports transcriptome assemblies for clustering work and traditional heat map, scatter plot, and line graph expression display.

Quick note: I do work for DNAStar as a Next-Gen App. Scientist, but you will find I'm no shill using this site. I actually find this site extremely valuable as a knowledge base for all of us. In this particular thread, however, these products do deserve notice.

[ECO]

Hey JKing,

Glad to have you! I swear I just read a paper using your software...ah yes...The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse....looks very interesting.

Got a couple of questions, as we're looking into this now...

Have you done any work with SOLiD data?

Any comments on how it runs assemblies on standalone desktop-y caliber machines?

[JKing]

Thanks for the warm welcome, Eco. This site is poised to be a valuable base of knowledge for all of us who are highly interested in this technology.

The best way for visitors of this site to get in depth information on SeqMan Genome Assembler (SGA), or to perform assemblies with their data, is to email info@dnastar.com. Like I said, I'm not here to hawk a product, but to continue to develop my own knowledge. Plus, posting technical specifics on a public forum runs the risk that the information will linger here and be old in a month when a new SGA version is released. Since you asked, however:

Have you done any work with SOLiD data?
SGA does accept and assemble csfasta files, and some of its specific trimming options for this data overcome some of the problems inherent in colorspace fasta files.

Any comments on how it runs assemblies on standalone desktop-y caliber machines?
SGA runs on 64 bit operating systems to eliminate any limits on RAM. For short read assemblies, it requires a computer with augmented (but not massively so) RAM. SGA is simply a command line assembler which provides .ace or .sqd output. All of the SNP filtering and codon analysis, as well as expression analysis, occurs in SeqMan Pro of the Lasergene suite and in ArrayStar, respectively (or in other software that accepts .ace files). The end user therefore does not require anything special computer-wise to perform the post-assembly analyses.

[ECO]

Excellent answers, and thanks for the feedback on the site. I'll be emailing soon.

[jhui]

SeqMap (http://biogibbs.stanford.edu/~jiangh/SeqMap/) - work like ELand, can do 3 or more bp mismatches and also insdel

[green tree]

Originally Posted by sci_guy

SNP/Indel Discovery
* ssahaSNP - ssahaSNP is a polymorphism detection tool. It detects homozygous SNPs and indels by aligning shotgun reads to the finished genome sequence. Highly repetitive elements are filtered out by ignoring those kmer words with high occurrence numbers. More tuned for ABI SOLiD reads. Developers are Adam Spargo and Zemin Ning from the Sanger Centre. Compaq Alpha, Linux-64, Linux-32, Solaris and Mac

Correct me if I am wrong, but I think that ssahaSNP is more tuned for ABI *Sanger* reads and not ABI SOLiD reads. For shorter reads, you can use ssaha2 (it even has a preconfigured option for Solexa) but you still have the problem of detecting SNPs and indels...

[RudyS]

anybody have scoops on possible software upgrade (GAP5?) for Staden package?

hoping
rudy

[Inti]

Does any of you guys have tryed the Genomatix products for Next Gen Seq?

[sparks]

First official release of novoalign & novopaired are now available for download at www.novocraft.com. Alignment with qualities and gaps for single end and paired end reads. small RNA mode, adapter stripping, trimming etc.
Can set number of mismatches from 0 to 8 (8 is only suitable on small genomes).
Fast
1M CElegans reads in 96s at ++2mismatches*
1M HSapiens reads in 32m at ++2mismatches*
*maybe more than two mismatches as result of quality based scoring
*single threaded 2.4Ghz CPU, 8Gb RAM
Free for non-commercial/open projects.

[ECO]

Hey Sparks...looks good. Appreciate the link from your homepage!

I will definitely take a close look at this...do you plan on supporting SOLiD data directly?

[sparks]

Hi ECO,
I'm not sure about ABI Solid. From what I've seen there's a lot of sequencing errors and paired end only does 25bp at each end and gets a really low yield (in terms of good alignments). Do you think it's important?