[jkbonfield]

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

I just noticed this forum - seems like a little gem :-)

Gap5 development is in progress, although it's slow as I keep getting distracted with SRF and ZTR trace formats. Currently there's not official public release of Gap5 itself, just of the text terminal viewer using some of the same code (see below).

So far the basic underlying storage and searching methods exist plus a basic contig editor. It's definitely fast and very efficient (both memory and cpu) compared to Gap4, but Gap4 has one key advantage - it's finished (as much as anything ever is)!

I should probably work on getting a publically useable release ready sometime, at least for testing purposes. The text-mode version which shares the same file format but is just a simple curses-based viewer can be downloaded from https://sourceforge.net/project/show...kage_id=256957 although it's a tad out of date.

James

[zee]

Looking good. This site is very useful. Will anybody in this community be getting together at the ISMB Toronto 2008 meeting?

[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?

[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]

Fast Short Read Aligner

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.

[Inti]

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

[RudyS]

STADEN - Includes GAP4. GAP5 once completed will handle next-gen sequencing data.

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

hoping
rudy

[green tree]

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...

[jhui]

one more

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

[ECO]

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

[JKing]

Nice to meet you, Eco

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 [email protected]. 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]

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]

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.

[tp_a]

thanks anthony for the info. will do for now.

A.

[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