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Forum: Bioinformatics 11-04-2010, 12:23 AM
Replies: 6
Views: 2,789
Posted By francesco.vezzi
The post is quite old and this approach was ...

The post is quite old and this approach was usufull do to the lack of software able to assembly mere than one lane.

The idea was to PARTITION (here is your point) in 10 or less independent...
Forum: Bioinformatics 11-03-2010, 12:51 AM
Replies: 6
Views: 2,789
Posted By francesco.vezzi
Hi. I think that the clustering must be made...

Hi.
I think that the clustering must be made before sequencing (by selecting specific regions of the genome using enzymes for example) and then assemble each small data set indepentetly.

The only...
Forum: Bioinformatics 08-25-2010, 07:23 AM
Replies: 27
Views: 11,200
Posted By francesco.vezzi
Hi, Mira is probably a good solution to your...

Hi,
Mira is probably a good solution to your problem. Two month ago I attended a conference in which one of the speakers was the Mira's author.
The tool is really good the only bad side is the...
Forum: Bioinformatics 08-25-2010, 12:24 AM
Replies: 4
Views: 2,879
Posted By francesco.vezzi
You are free to treat the reads as they are...

You are free to treat the reads as they are singletons but this will probably lead to a bad assembly with a lot of short contigs. If you have a way to keep the paired read information (with the SAM...
Forum: Bioinformatics 08-23-2010, 11:27 PM
Replies: 2
Views: 1,550
Posted By francesco.vezzi
It depends on the format. Illumina produces two...

It depends on the format. Illumina produces two file s_1_1_sequences.txt and s_1_2_sequences.txt . The first read in the first file is in mate relationship with the first read in the second file....
Forum: Bioinformatics 08-23-2010, 02:49 AM
Replies: 3
Views: 5,307
Posted By francesco.vezzi
MIRA3 is probably what you need... Remember...

MIRA3 is probably what you need...
Remember that SOAPdenovo gives as output a file named *.scafSeq that contains the scaffolds (from my experience the contig file contains a lot of very short and...
Forum: Bioinformatics 08-19-2010, 12:19 AM
Replies: 10
Views: 4,095
Posted By francesco.vezzi
Hi natstreet there is a thing that I don't...

Hi natstreet
there is a thing that I don't understand about Curtain. It is a reference assisted assembler (it uses maq to align reads against a reference and then if improved the reference assembly)...
Forum: Bioinformatics 08-18-2010, 11:18 PM
Replies: 10
Views: 4,095
Posted By francesco.vezzi
I think that a solution to your problem is use...

I think that a solution to your problem is use SOAPdenovo or ABySS that have lower memory requirements

Francesco
Forum: Bioinformatics 07-04-2010, 11:26 PM
Replies: 35
Views: 12,694
Posted By francesco.vezzi
Hi at the end it seems that nobody is able to...

Hi
at the end it seems that nobody is able to run ALLPATHS is that true?

F.
Forum: Bioinformatics 07-04-2010, 11:20 PM
Replies: 1
Views: 2,775
Posted By francesco.vezzi
Hi, SOAPdenovo: probably the data structures...

Hi,
SOAPdenovo: probably the data structures used by SOAPdenovo became too large with such big kmer, actually I'm a bit surprised that velvet is able to run with a kmer of size 47....
Another...
Forum: Bioinformatics 06-01-2010, 03:12 AM
Replies: 35
Views: 12,694
Posted By francesco.vezzi
Hi I spend one week trying to install ALLPATHS...

Hi
I spend one week trying to install ALLPATHS without results. It seems that the source code is designed to be compiled only on the machines of the authors... I never heard somebody that was able...
Forum: Bioinformatics 05-27-2010, 03:00 AM
Replies: 7
Views: 3,473
Posted By francesco.vezzi
Yes I contact them more than once.... but they...

Yes I contact them more than once.... but they never reply...
It is really strange that the most used aligner (or at least one of the most used) is so obscure.....
Forum: Bioinformatics 05-27-2010, 02:53 AM
Replies: 7
Views: 3,473
Posted By francesco.vezzi
Hi I can't help you so much but I can report...

Hi
I can't help you so much but I can report another strange behaviour of SOAP2. Despite the fact that you vary the -v option that is the total amount of errors (mismatches) allowed in one read the...
Forum: De novo discovery 05-17-2010, 12:28 AM
Replies: 1
Views: 2,263
Posted By francesco.vezzi
mixing long and short sequences

Hi all
I'm trying to assembly a plant genome using a 70X coverage formed by Illumina reads (75 bases). Some days ago it turned out that we have also a set of Sanger paired reads belonging to the...
Forum: Bioinformatics 05-16-2010, 08:07 AM
Replies: 278
Views: 116,972
Posted By francesco.vezzi
Ray and genome size

Hi Seb
your assembler seems really promising. I was wondering if it able to work also with plant and animals genomes that have the problem to be really long (Gigabases) and to have really long...
Forum: 454 Pyrosequencing 05-13-2010, 12:08 AM
Replies: 3
Views: 4,167
Posted By francesco.vezzi
HI Newbler is definitely base on the Overlap...

HI
Newbler is definitely base on the Overlap Layout Consensus methodology. I suggest to you to read the survey "Assembly algorithms for next-generation sequencing data." by Miller.

Newbler works...
Forum: Bioinformatics 04-29-2010, 01:44 AM
Replies: 10
Views: 4,339
Posted By francesco.vezzi
I'm assembling a grapevine clone. The reference...

I'm assembling a grapevine clone. The reference genome length is 400MB. SOAPdenovo is divided in several step. The read correction takes approximately 1 day. The denovo step takes 5 hours while the...
Forum: Bioinformatics 04-26-2010, 11:31 PM
Replies: 10
Views: 4,339
Posted By francesco.vezzi
Hi I think that the best way to deal with this...

Hi
I think that the best way to deal with this huge amount of data is use one between SOAPdenovo and ABySS. With them I'm able to assembly 16 illumina lanes with less then 80Giga ram memory.

...
Forum: Bioinformatics 02-15-2010, 06:49 AM
Replies: 2
Views: 2,601
Posted By francesco.vezzi
Every time you start from the same reference...

Every time you start from the same reference sequence or you iteratevely reuse the result of the previous step? I mean do you first align with three errors and then you use the consensus that you...
Forum: De novo discovery 02-11-2010, 08:07 AM
Replies: 2
Views: 2,238
Posted By francesco.vezzi
In the manual there is a description of how...

In the manual there is a description of how generate an histogram that can help you in decide several parameters.
In general the best way to proceed is make some test on a little data set. You keep...
Forum: Bioinformatics 01-06-2010, 08:50 AM
Replies: 12
Views: 19,150
Posted By francesco.vezzi
In order to assmebly a lane of paired reads of...

In order to assmebly a lane of paired reads of length 75 we used 120 giga with a k-mer size of 47.
Obviously the amount of date decrease with a smaller k-mer, but a shorter k-mer implies a higher...
Forum: De novo discovery 11-17-2009, 12:15 AM
Replies: 1
Views: 4,721
Posted By francesco.vezzi
This is usually true but if the more you produce...

This is usually true but if the more you produce is meaningless it is only a waste. For example one year ago we produce with the kit of 36 bases experiments of 45 bases with the result that we where...
Forum: General 11-06-2009, 02:35 AM
Replies: 8
Views: 7,943
Posted By francesco.vezzi
OK... first of all in the lab where I work we...

OK... first of all in the lab where I work we have an Illuminna GAII, and I never work on other kind of data....

I can try to answer your question in the following way: the success of illumina are...
Forum: Bioinformatics 11-02-2009, 11:44 PM
Replies: 27
Views: 11,200
Posted By francesco.vezzi
Until now I had good results using a subset of...

Until now I had good results using a subset of the generated reads. Your bad result can depend on several reasons.

I can try to suggest something like filter the low quality reads and trim the...
Forum: Bioinformatics 10-29-2009, 01:19 AM
Replies: 27
Views: 11,200
Posted By francesco.vezzi
Hi all, I read this intresting topic. There are...

Hi all,
I read this intresting topic. There are two main discussions the first is about the definitation of a proper tool able to assemble the trancriptome, the second is about the memory...
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