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Old 01-23-2009, 12:38 AM   #101
francesco.vezzi
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Thanks to both,
the file present in the supplementary material is too old... i have already send an email to the authors and they said that as soon as possible they would put on line the new version but this is happened some month ago...

The thing that surprise me is that all the articles on de novo ASSEMBLY cite this instrument, but I never saw experimental result about it except in the article of ALLPATHS....
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Old 01-23-2009, 12:10 PM   #102
RudyS
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likewise there is no download available on the main page
http://www.broad.mit.edu/science/pro...nd-development

though they state that it is available

but they also indicate that allpaths has only been tested with simulated data ... so maybe better to wait til its been tested on something real?

rudyS
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Old 01-25-2009, 10:37 PM   #103
francesco.vezzi
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Yes for sure is better way it is tested on a real data set, the thing that it seems strange to me is the fact that in the last year I found dozen of articles that cite ALLPATH as an excellent assembler but it seems that nobody has effectively used it....
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Old 01-26-2009, 03:02 AM   #104
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I am trying to realize an assembly of sequences (454 + Sanger) of novo using the program wgs-assembler (Celera Assembler). This program needs a file *.frg to begin the assembly. Can someone obtain like the file *.frg from the files *.fasta and *.qual without using the file *.xml?.

Thank you for everything.

Rocio
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Old 02-14-2009, 08:24 PM   #105
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Default Most conservative aligner

I wish to find the best alignment of my 32bp and 100bp reads (separately, not as single input), and also determine the next best matches. Which algorithm would be most suitable for this purpose?

I understand that it can take longer to run, than some of the other algorithms that run much faster..

Any thoughts?
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Old 02-15-2009, 08:36 AM   #106
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Default Suboptimal hits

Novoalign will do this for you. You might have to play around with the parameters to get exactly what you want (how many suboptimal hits, how suboptimal etc).

Ryan
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Old 02-16-2009, 09:59 AM   #107
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I think that Bowtie will also return the optimal and sub-optimal matches.

Bowtie is a BWA program, that's the algorithm that the fastest aligners are based on.
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Old 02-25-2009, 12:54 PM   #108
jerryliu
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Quote:
Originally Posted by rociobm View Post
I am trying to realize an assembly of sequences (454 + Sanger) of novo using the program wgs-assembler (Celera Assembler). This program needs a file *.frg to begin the assembly. Can someone obtain like the file *.frg from the files *.fasta and *.qual without using the file *.xml?.

Thank you for everything.

Rocio
There is a script FASTA_to_frg_file.pl under Linux-amd64/bin/ that can convert fasta to .frg file.
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Old 03-04-2009, 04:50 AM   #109
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I didn't see MACS and PeakSeq among the ChIP-seq peak callers. Those should be added.
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Old 03-04-2009, 06:55 AM   #110
bioinfosm
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Default SHORE (SHOrt REads)

It is an impressive package .. with a lot of statistics and pretty plots generated at the end of analysis. Wonder why no one catched it here.

http://1001genomes.org/downloads/

Now my query is, how it matches up to MAQ and others.. it is pretty fast though
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Old 03-09-2009, 12:01 AM   #111
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Default SeqCons

A Consistency-based Consensus Algorithm for De Novo and Reference-guided Sequence Assembly of Short Reads

http://www.seqan.de/projects/consensus.html

Bioinformatics Advance Access published March 5, 2009
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Old 03-09-2009, 12:05 AM   #112
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Default ABySS (Assembly By Short Sequences)

http://www.bcgsc.ca/platform/bioinfo/software/abyss

Genome Res. 2009 Feb 27.

ABySS: A parallel assembler for short read sequence data.

Widespread adoption of massively parallel DNA sequencing instruments has prompted the recent development of de novo short read assembly algorithms. A common shortcoming of the available tools is their inability to efficiently assemble vast amounts of data generated from large-scale sequencing projects, such as the sequencing of individual human genomes to catalog natural genetic variation. To address this limitation, we developed ABySS (Assembly By Short Sequences), a parallelized sequence assembler. As a demonstration of the capability of our software, we assembled 3.5 billion paired-end reads from the genome of an African male publicly released by Illumina Inc. Approximately 2.76 million contigs >/=100bp in length were created with an N50 size of 1499bp, representing 68% of the reference human genome. Analysis of these contigs identified polymorphic and novel sequences not present in the human reference assembly, which were validated by alignment to alternate human assemblies and to other primate genomes

http://www.ncbi.nlm.nih.gov/pubmed/1...?dopt=Abstract
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Old 03-11-2009, 12:27 PM   #113
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Default LookSeq: ALignment visualization

from Sanger
http://www.sanger.ac.uk/Software/analysis/lookseq/
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Old 03-11-2009, 04:45 PM   #114
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Hi everyone,

I'm new to NGS. I'm looking for a software package to analyze the sequences. Are there any review articles about the softwares?

Thanks,
Jack
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Old 03-12-2009, 09:46 AM   #115
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Default Staden GAP5

i note that there is no active link in the posting

* STADEN - Includes GAP4. GAP5 once completed will handle next-gen sequencing data. A partially implemented test version is available here

anybody have news about GAP5? havent found a satisfying assembler with graphics

RudyS
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Old 03-12-2009, 12:14 PM   #116
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Quote:
Originally Posted by RudyS View Post
i note that there is no active link in the posting

* STADEN - Includes GAP4. GAP5 once completed will handle next-gen sequencing data. A partially implemented test version is available here

anybody have news about GAP5? havent found a satisfying assembler with graphics

RudyS
They've been saying that gap5 will handle short reads for about a year, so I wouldn't hold your breath on that one.

If you are doing mouse or human or rat, UCSC can be worked with. I don't know if it can be tweaked into accepting genomes or trasncriptomes of other organisms.
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Old 03-12-2009, 06:22 PM   #117
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swbarnes

are you saying that there is some utility in the UCSC Genome Browser for assembling genomes from short reads? havent heard about that ...

RudyS
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Old 03-13-2009, 01:53 PM   #118
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Quote:
Originally Posted by RudyS View Post
swbarnes

are you saying that there is some utility in the UCSC Genome Browser for assembling genomes from short reads? havent heard about that ...

RudyS
It's not assembly, it would be more like alignment, and I think I heard this is doable, but I don't work with any of the organisms they have there, so I didn't investigate for myself.
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Old 03-14-2009, 07:49 AM   #119
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thanks swbarnes2

i think i will post a query on the UCSC listserver
[email protected]
and see if someone like Jim Kent is thinking about some utility that could facilitate reference assembly on a local Genome Browser ... he's the guy i think who initiated BLAT and isPCR on their site

http://genome.ucsc.edu/

the browser can be installed locally and used with any genome ... but without taking into account quality values from the reads its hard to imagine not getting just a mess doing a BLAT-like alignment ... i think

RudyS
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Old 03-20-2009, 08:50 AM   #120
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Quote:
Originally Posted by rs705 View Post
DNASTAR has changed the name of its integrated tool from SeqMan Genome Assembler to SeqMan NGen. it also works on Vista since that it what we are using with it.
I would be interested to know how DNASTAR Seqman NGen does with ChIP-Seq as well as DGE alignments. I need to get data to complete neophytes off of all these platforms. Horsepower and speed could take back seat to "ease of use" since each user will be getting just a portion of a complete run.

Any other packages that qualify as "easy to use" out there? Can any of them handle SRF files from a Helicos too?

I know, not asking for much. Can it filter RAW and tie my shoes also?
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