Software packages for next gen sequence analysis

[bioinfosm]

GeoSpiza

Anyone heard of them? or their suite of tools for next gen data analysis, visualization and management?

[ECO]

Anyone heard of them? or their suite of tools for next gen data analysis, visualization and management?

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

[bioinfosm]

parsing the output

How are people making use of outputs from various tools?

For instance
soap has this one line format with its way of representing variation
shrimp seems even more complicated with a fasta line format not even mentioning where the substitutions / indels are ... even if you look at the prettyplot

Any views on visualizing the data on global scale .. giving an indication of depth of sequencing at various regions on the reference, % variation... etc?

[apfejes]

To answer the part on visualization, I have several tools that create files that are viewable on the UCSC genome browser. or generate a text file showing the aligned reads against the canonical sequence. I now even have a tool for generating post script files of peaks (for Chip-Seq experiments) along entire chromosomes.

The question is really what you're looking for. It's easy to visualize this data, but very hard to create new views that give new insight.

[bioinfosm]

To answer the part on visualization, I have several tools that create files that are viewable on the UCSC genome browser. or generate a text file showing the aligned reads against the canonical sequence. I now even have a tool for generating post script files of peaks (for Chip-Seq experiments) along entire chromosomes.
The question is really what you're looking for. It's easy to visualize this data, but very hard to create new views that give new insight.

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

[todd]

Who is Geospiza?

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]

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]

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]

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]

ace files from MAQ or SOAP alignment viewable in EagleView

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]

findpeaks s/w

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]

Sga

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.