ABI Paired End Reads

sparks · 06-15-2010, 04:45 PM

Hi,
Does anyone have information on the new ABI Paired end reads, especially file formats and orientations of the reads.

We are developing a colour space version of Novoalign that's performing pretty well but we would like to support paired end as well as mate pair for first release and having some sample data would help a lo, let us know if you have some reads to share, we don't need many.

If anyone would like to try beta of NovoalignCS just ask.

Colin

epigen · 06-16-2010, 05:08 AM

NovoalignCS sounds great. I'm currently comparing the performance of BWA and BioScope on SOLiD transcriptome data (single end, unfortunately). Having Novoalign as a third option would be nice, especially since other people in my group are happy using it on their non-colorspace reads. I always stumble across all kinds of bugs anyway, so volunteering as a beta tester seems obvious.

sparks · 06-16-2010, 06:38 AM

hi epigen,

That would be great if you could help. Just email me at colin at novocraft dot com I'll send you necessary info.

Colin

nilshomer · 06-16-2010, 11:51 AM

I have found novoalignCS very sensitive and specific when the alignments are evaluated after variant calling (SAMtools). I would definitely recommend testing this alignment tool, although it may be a little slow (like the regular novoalign) if you have 10+ sequencers (talking to you Broad/Baylor/WashU/etc.). Otherwise the multi-threaded version is the way to go, with MPI if you have it installed.

One issue is that the # of reads from a SOLiD slide is in the hundreds of millions. If you don't have MPI installed, and you still want to align the many reads from a SOLiD run in a parallel fashion, I have created a script to convert and split the reads after using the "solid2fastq" utility in BFAST. It's a perl script, but is renamed with a .txt extension to fool the HTTP server:
http://genome.ucla.edu/~nhomer/novoa...bfast2novo.txt
You can use this in a piped fashion:

Code:

solid2fastq [options] <csfastas> <quals> | bfast2novo.pl - <out.prefix> <split num>

Hopefully this will help those with idle machines fill them up with novoalignCS.

Rao · 06-16-2010, 11:06 PM

data set is available on solidsoftwarecommunity.com

KevinLam · 06-17-2010, 11:47 PM

Hmmm why not approach ABI for the sample data sets?
with SOLiD4 being the new standard you might get different results if u used old datasets

sparks · 09-20-2010, 02:01 AM

Thanks for help and suggestions. e managed to get a few files of Colour space paired end reads and latest versions of NovoalignCS now fully support paired end and mate pair reads.

Colin

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06-15-2010, 04:45 PM	#1
sparks Senior Member Location: Kuala Lumpur, Malaysia Join Date: Mar 2008 Posts: 113	ABI Paired End Reads Hi, Does anyone have information on the new ABI Paired end reads, especially file formats and orientations of the reads. We are developing a colour space version of Novoalign that's performing pretty well but we would like to support paired end as well as mate pair for first release and having some sample data would help a lo, let us know if you have some reads to share, we don't need many. If anyone would like to try beta of NovoalignCS just ask. Colin

06-16-2010, 11:51 AM	#4
nilshomer Super Moderator Location: Boston, MA, USA Join Date: Nov 2008 Posts: 1,279	I have found novoalignCS very sensitive and specific when the alignments are evaluated after variant calling (SAMtools). I would definitely recommend testing this alignment tool, although it may be a little slow (like the regular novoalign) if you have 10+ sequencers (talking to you Broad/Baylor/WashU/etc.). Otherwise the multi-threaded version is the way to go, with MPI if you have it installed. One issue is that the # of reads from a SOLiD slide is in the hundreds of millions. If you don't have MPI installed, and you still want to align the many reads from a SOLiD run in a parallel fashion, I have created a script to convert and split the reads after using the "solid2fastq" utility in BFAST. It's a perl script, but is renamed with a .txt extension to fool the HTTP server: http://genome.ucla.edu/~nhomer/novoa...bfast2novo.txt You can use this in a piped fashion: Code: solid2fastq [options] <csfastas> <quals> \| bfast2novo.pl - <out.prefix> <split num> Hopefully this will help those with idle machines fill them up with novoalignCS. Last edited by nilshomer; 06-16-2010 at 11:51 AM. Reason: Must fool the HTTP server

06-17-2010, 11:47 PM	#6
KevinLam Senior Member Location: SEA Join Date: Nov 2009 Posts: 188	Hmmm why not approach ABI for the sample data sets? with SOLiD4 being the new standard you might get different results if u used old datasets __________________ http://kevin-gattaca.blogspot.com/

06-16-2010, 05:08 AM	#2
epigen Senior Member Location: Germany Join Date: May 2010 Posts: 101	NovoalignCS sounds great. I'm currently comparing the performance of BWA and BioScope on SOLiD transcriptome data (single end, unfortunately). Having Novoalign as a third option would be nice, especially since other people in my group are happy using it on their non-colorspace reads. I always stumble across all kinds of bugs anyway, so volunteering as a beta tester seems obvious.

06-16-2010, 06:38 AM	#3
sparks Senior Member Location: Kuala Lumpur, Malaysia Join Date: Mar 2008 Posts: 113	hi epigen, That would be great if you could help. Just email me at colin at novocraft dot com I'll send you necessary info. Colin

06-16-2010, 11:06 PM	#5
Rao Member Location: India Join Date: Oct 2008 Posts: 36	data set is available on solidsoftwarecommunity.com

09-20-2010, 02:01 AM	#7
sparks Senior Member Location: Kuala Lumpur, Malaysia Join Date: Mar 2008 Posts: 113	Thanks for help and suggestions. e managed to get a few files of Colour space paired end reads and latest versions of NovoalignCS now fully support paired end and mate pair reads. Colin