454 ACE assembly with paired reads... how to view?

susanklein · 02-10-2014, 04:13 AM

Hi,

I'm new here, thanks in advance for any help.

I have a 454 dataset of 'allcontigs.ace'. The reads consist of paired and unpaired. If I use a viewer like Tablet, which I find very good.. I can see the paired reads in the contigs and which other contigs they are paired to etc. but I cannot see the corresponding orientation of those contigs.. I should say, I am trying to examine a 'chain' of contigs out from one of interest, none of which have been included in the scaffold (because they originate from a 16S sequence). So my question is.. is there a viewer I can use which will show the contigs and their relative orientation, based on the paired reads they share?

I have tried several so far with no luck.

Thanks very much,

S.

mastal · 02-10-2014, 05:57 AM

What viewers have you tried?

Have you tried Hawkeye, it is part of the Amos package?

susanklein · 02-10-2014, 11:12 AM

Hi,

I tried Eagle, Consed (couldn't install), Tablet, Magicviewer. Tablet does show the orietation of each paired read.. The more I think about it, that should be enough, but it would be nice to view the 'joined' contigs together. I will try amos.

Thanks,

S.

sklages · 02-10-2014, 10:04 PM

If you want to edit the assembly (e.g. move contigs around etc.) I'd recommend consed. Installation is not really complicated and very well documented. Newbler, gsAssembler, is able to produce a complete consed folder. This has to be checked before the actual (denovo) assembly.

If it is just for viewing the paired reads information / contig layout, Hawkeye is the way to go :-)

my 2p,
Sven

susanklein · 02-10-2014, 10:11 PM

Thanks Sven, I followed the consed docs on installation and wasted a day in the attempt.. error after error.. so don't have time for it. Need results. I'll try the other progs.
Thx again.
S.

maubp · 02-12-2014, 01:34 AM

Quote:

Originally Posted by susanklein

I have a 454 dataset of 'allcontigs.ace'. The reads consist of paired and unpaired. If I use a viewer like Tablet, which I find very good.. I can see the paired reads in the contigs and which other contigs they are paired to etc.

You'd have to convert your assembly into SAM/BAM if you want Tablet (or most other assembly viewers) to show the pairing. That conversion might be possible with GAP5...

Also Newbler had some experimental BAM output support - I'm not sure if it was ever properly finished and working though.

susanklein · 02-12-2014, 01:40 AM

Quote:

Originally Posted by maubp

You'd have to convert your assembly into SAM/BAM if you want Tablet (or most other assembly viewers) to show the pairing. That conversion might be possible with GAP5...

Also Newbler had some experimental BAM output support - I'm not sure if it was ever properly finished and working though.

hey, thanks. yes I thought I'd need to convert it but that prob means doing the assembly again and I'll have to fish out the paired and unpaired reads (mixed in the. sff) But I'll get around to it.
Thanks for the advice.

S.

maubp · 02-12-2014, 01:51 AM

You could also try 454 assembly with MIRA4 which has SAM output (or you can convert MIRA's own output into SAM).

sklages · 02-12-2014, 01:58 AM

Quote:

Originally Posted by maubp

You could also try 454 assembly with MIRA4 which has SAM output (or you can convert MIRA's own output into SAM).

There are quite a few options to "optimize" this process ... but it's always a problem, when there is no time and things just "need to get done"..

But I agree, .. with MIRA4 you gain more flexibilty. E.g. Staden's gap4/5 :-)

maubp · 02-12-2014, 02:01 AM

The other option is to hunt for a working ACE to SAM/BAM converter which handles the paired information - people have tried this before but I'm not sure if there is a complete solution.

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02-10-2014, 04:13 AM	#1
susanklein Senior Member Location: oceania Join Date: Feb 2014 Posts: 115	454 ACE assembly with paired reads... how to view? Hi, I'm new here, thanks in advance for any help. I have a 454 dataset of 'allcontigs.ace'. The reads consist of paired and unpaired. If I use a viewer like Tablet, which I find very good.. I can see the paired reads in the contigs and which other contigs they are paired to etc. but I cannot see the corresponding orientation of those contigs.. I should say, I am trying to examine a 'chain' of contigs out from one of interest, none of which have been included in the scaffold (because they originate from a 16S sequence). So my question is.. is there a viewer I can use which will show the contigs and their relative orientation, based on the paired reads they share? I have tried several so far with no luck. Thanks very much, S.

02-10-2014, 05:57 AM	#2
mastal Senior Member Location: uk Join Date: Mar 2009 Posts: 666	What viewers have you tried? Have you tried Hawkeye, it is part of the Amos package?

02-10-2014, 11:12 AM	#3
susanklein Senior Member Location: oceania Join Date: Feb 2014 Posts: 115	Hi, I tried Eagle, Consed (couldn't install), Tablet, Magicviewer. Tablet does show the orietation of each paired read.. The more I think about it, that should be enough, but it would be nice to view the 'joined' contigs together. I will try amos. Thanks, S.

02-10-2014, 10:04 PM	#4
sklages Senior Member Location: Berlin, DE Join Date: May 2008 Posts: 628	If you want to edit the assembly (e.g. move contigs around etc.) I'd recommend consed. Installation is not really complicated and very well documented. Newbler, gsAssembler, is able to produce a complete consed folder. This has to be checked before the actual (denovo) assembly. If it is just for viewing the paired reads information / contig layout, Hawkeye is the way to go :-) my 2p, Sven

02-10-2014, 10:11 PM	#5
susanklein Senior Member Location: oceania Join Date: Feb 2014 Posts: 115	Thanks Sven, I followed the consed docs on installation and wasted a day in the attempt.. error after error.. so don't have time for it. Need results. I'll try the other progs. Thx again. S.

02-12-2014, 01:51 AM	#8
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	You could also try 454 assembly with MIRA4 which has SAM output (or you can convert MIRA's own output into SAM).

02-12-2014, 02:01 AM	#10
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	The other option is to hunt for a working ACE to SAM/BAM converter which handles the paired information - people have tried this before but I'm not sure if there is a complete solution.