[paa6]

In case you have not discovered these already:

http://res.illumina.com/documents/pr...mbly_ecoli.pdf

http://www.nature.com/nbt/journal/v29/n11/abs/nbt.2023.html

http://www.biostars.org/p/52178/

hey thanks a lot...I have read them though...and I am using geneious software for assembly...

[GenoMax]

In case you have not discovered these already:

http://res.illumina.com/documents/pr...mbly_ecoli.pdf

http://www.nature.com/nbt/journal/v29/n11/abs/nbt.2023.html

http://www.biostars.org/p/52178/

[paa6]

@paa6: Before you spend a lot of time on this "assembly" what size genome are you working on? How much data do you have ("x" fold coverage based on the expected genome size)? Unless you have enough data available you may not be able to do a reasonable/sussessful assembly.

yeah u r right...and since I am new in de novo assembly I dont understand these terms at all...and right now I have to analyse contigs what I have got from illumina....I am slow because I am learning and then sooner after that I have to start 454 assembly...I will take note on ur questions...and will discuss with u sooner...

[GenoMax]

@paa6: Before you spend a lot of time on this "assembly" what size genome are you working on? How much data do you have ("x" fold coverage based on the expected genome size)? Unless you have enough data available you may not be able to do a reasonable/sussessful assembly.

[paa6]

.. still wondering why you don't have a look at the manual and/or ask geneious support team ..

actually currently I am working on illumina assembly..dont have time for .sff file..because my supervisor want it done first..so when I will start working on .sff, I will let u know...and try everything whatever u have suggested...thanks a lot..

[sklages]

.. still wondering why you don't have a look at the manual and/or ask geneious support team ..

[paa6]

Here is an example SFF file: http://www.ncbi.nlm.nih.gov/sra?term...0cluster_dbgap (click on the "size" to download).

As I said before this particular file will be in .sra format (which is a special format that SRA uses). You will have to use sff-dump program found in the SRA-toolkit: http://www.ncbi.nlm.nih.gov/Traces/s...?view=software to convert the .sra file to the original SFF format.

THANK U SO MUCH i WILL TRY THAT...

[GenoMax]

I did try that but I couldnt found..ok I will try again...

Here is an example SFF file: http://www.ncbi.nlm.nih.gov/sra?term...0cluster_dbgap (click on the "size" to download).

As I said before this particular file will be in .sra format (which is a special format that SRA uses). You will have to use sff-dump program found in the SRA-toolkit: http://www.ncbi.nlm.nih.gov/Traces/s...?view=software to convert the .sra file to the original SFF format.

[GenoMax]

thanks a lot....but the thing is that I tried this link but other sites r getting opened on the same page...

See the README: http://www.ibi.vu.nl/downloads/454CO...rchives.README

Download one of the files (> 2G file) : http://www.ibi.vu.nl/downloads/CORE_1.tar.gz

[paa6]

Hi,

In case you don't mind them being generated by a simulation software, I've recently uploaded many 454Sim-generated SFFs under http://www.ibi.vu.nl/downloads/, see the section 454 data used in and the corresponding readme file.

Cheers

thanks a lot....but the thing is that I tried this link but other sites r getting opened on the same page...

[paa6]

For the general ability to read SFF files you should ask the support team of your software and/or look at their website and have a look at the manual.

To check if your SFF file is corrupt you can either

a) use 'strings' and see if the file ends with readnames
b) use sffinfo from the Roche SFF Tools to see, if the file can be read/parsed. If not, you'll get an error and you can be sure that your file is corrupted (as the SFF Tools are definitely able to read SFF files :-) )

hth

thanks a lot...I will try this...

[paa6]

You should be able to find SFF files on NCBI-SRA. http://www.ncbi.nlm.nih.gov/sra They will be in SRA format (search for 454 datasets). You will then have to convert them into SFF.

I did try that but I couldnt found..ok I will try again...

[harlequin]

I already have .sff file but I guess that is corrupted but still I want to check that whether my software is able to import .sff file or not....

I am working on geneious software. So, I have tried a lot to download any random file in .sff format so that I can try to import in geneious but I didn't get it from anywhere.

Hi,

In case you don't mind them being generated by a simulation software, I've recently uploaded many 454Sim-generated SFFs under http://www.ibi.vu.nl/downloads/, see the section 454 data used in and the corresponding readme file.

Cheers

[sklages]

I already have .sff file but I guess that is corrupted but still I want to check that whether my software is able to import .sff file or not....

I am working on geneious software. So, I have tried a lot to download any random file in .sff format so that I can try to import in geneious but I didn't get it from anywhere.

For the general ability to read SFF files you should ask the support team of your software and/or look at their website and have a look at the manual.

To check if your SFF file is corrupt you can either

a) use 'strings' and see if the file ends with readnames
b) use sffinfo from the Roche SFF Tools to see, if the file can be read/parsed. If not, you'll get an error and you can be sure that your file is corrupted (as the SFF Tools are definitely able to read SFF files :-) )

hth

[GenoMax]

You should be able to find SFF files on NCBI-SRA. http://www.ncbi.nlm.nih.gov/sra They will be in SRA format (search for 454 datasets). You will then have to convert them into SFF.