Input files for the Celera Assembler?

[dan]

Hi,

I have sequence reads as a fasta file with a fasta quality file. I am converting these into .frg input for the Celera Assembler (CA) using AMOS,

toAmos -s test.fasta -q test.qual -o test.afg

and then:

amos2frg -i test.afg

However, the above strategy does not recognize the 'mate pairs' in my data (paired end reads) that are 'linked' using the St Louis naming convention (basically read0012.b is pared with read0012.g, the .b and the .g denoting the forward and the backward read, respectively).

On the AMOS mailing list I got a reply to a similar question from Sven Klages, which told me that CA is usually passed a separate "linkage information" file in addition to the .frg input created above. His suggestion was to create linkage data in 'Trace Archive' format*, and then convert that to input for CA using AMOS again.

Has anyone tackled this problem before? Is there any code 'off the shelf' to create the mate pair data?


* http://www.ncbi.nlm.nih.gov/Traces/t...#header-global


Cheers,
Dan.


P.S. Any other good mailing lists for sequence assembly?

If you know any, I'll add them here:

http://biodatabase.org/index.php/List_of_mailing_lists_for_biologists

[new300]

Are you planning to use the Celera assembler with short reads? Because I don't think it would work very well.

[sklages]

@Dan,

my suggestion was to either use the bambus mate pair output or a TraceArchive formatted XML file for use with "toAmos", like

$ toAmos -s x.fasta -q x.qual -m test.mates -o test.a.afg

or

$ toAmos -s x.fasta -q x.qual -x test.xml -o test.a.afg

but, of course, you have to create these files before.

It is probably the easiest way to write your own "your_data2TraceArchive.pl" and then convert it to whatever you want, e.g. CA format using "tracedb-to-frg.pl".

@new300,

Celera Assembler has been optimised for at least 454FLX length reads; I have used it for shorter GS20 as well, but it may fail. All these assemblies were hybrid assemblies, not 454-only ones.

hth,
Sven

[new300]

Celera Assembler has been optimised for at least 454FLX length reads; I have used it for shorter GS20 as well, but it may fail. All these assemblies were hybrid assemblies, not 454-only ones.

That's interesting, I'm surprised it copes with the elevated indel/homopolymer run error rate.

[dan]

@Dan,

my suggestion was to either use the bambus mate pair output or a TraceArchive formatted XML file for use with "toAmos", like

$ toAmos -s x.fasta -q x.qual -m test.mates -o test.a.afg

or

$ toAmos -s x.fasta -q x.qual -x test.xml -o test.a.afg

but, of course, you have to create these files before.

It is probably the easiest way to write your own "your_data2TraceArchive.pl" and then convert it to whatever you want, e.g. CA format using "tracedb-to-frg.pl".

Yeah, that's what I'm struggling with... Any reference for the bambus format on the off chance that its simpler? I can't help thinking there is a canned solution in the AMOS docs if only I could find it.

[dan]

Seems the Bambus docs will help:

http://amos.sourceforge.net/docs/bambus/Manual.html

[sklages]

Yeah, that's what I wanted to send just about now

http://amos.sourceforge.net/docs/bambus/Manual.html#matesfile

Btw,. I meant Bambus *input* not output ...

cheers,
Sven

[dan]

Sadly it doesn't seem to be working...

toAmos -s x.fasta -q x.qual  -o a.afg

toAmos -s x.fasta -q x.qual -m test.mates -o b.afg

Gives:

diff a.afg b.afg
5c5
< Thu Dec  4 12:24:40 2008
---
> Thu Dec  4 12:27:07 2008

Following the info on the link I set test.mates to the following:

pair	\W+\.b\.abi	\W+\.g\.abi

Their is no error on either command.

[dan]

I should try before I reply... Setting test.mates to

pair	\.b\.abi	\.g\.abi

Seems to have had the desired effect!

Now I just need to rerun the assembly and check in hawkeye.

[sklages]

pair    \W+\.b\.abi    \W+\.g\.abi

If this is a perl RE "\W+" means, "everything but chars, digits and _"; that is
probably not what you want.

Your sample name looks like this: 065I03X00001.b.abi

better this way (\t as separator):

 pair  (.*)\.b\.abi$ (.*)\.g\.abi$

hth,
Sven

[dan]

Are you planning to use the Celera assembler with short reads? Because I don't think it would work very well.

Have a look here,

http://seqanswers.com/forums/showthread.php?t=719&highlight=celera

[gengen]

How to create frg file from SRA data ?

I want to run Celera Assembler usign SRA 454 data, but SRA doesn't provide sff data. They only provide FASTA and FASTQ.
So, how should I do ? I could do this by coverting FASTQ to FASTA and quality file and then converting them to frg file, but this is so roundabout and also I must write some scripts. Let me know if you have any idea for this issue.

thanks in advance

[novice2]

To all members

Dear All

My pcr assay has suddenly began producing these curious strutures-- I have attached an image to show this effect. Can anyone explain please what mat be going on and what I can do to get rid of it. Before this the pcr was working fine.

[novice2]

To all members

I have attached a further 2 images showing this effect.

[sklages]

@gengen,

Have a look at Celera Input Formatting

Sven