Re: [galaxy-dev] SeqPrep wrapper?

2013-10-23 Thread Lionel Guy

Hi Brad and all,

To follow-up on this, I've released a SeqPrep wrapper, v0.1:

http://toolshed.g2.bx.psu.edu/view/lionelguy/seqprep

Any testing and report is highly appreciated!

Cheers,

Lionel

On 10/14/2013 01:55 PM, Lionel Guy wrote:

Hi Brad,

(cc-ing the list)

I'm more interested in the merging part, and after a quick search on the 
toolshed, there are no tools to merge reads. Seems that there is a need for a 
read merger wrapper then...

Lionel

On 14 Oct 2013, at 13:46 , Langhorst, Brad langho...@neb.com wrote:


I would also like to see a seqprep wrapper…
if you need something sooner, cutdadapt is already wrapped and i'm pretty sure 
there is an existing tool to merge reads as well.

Brad
--
Brad Langhorst
Applications and Product Development Scientist

On Oct 14, 2013, at 6:59 AM, Lionel Guy guy.lio...@gmail.com
wrote:


Hi,

I'm interested in a wrapper for SeqPrep:
https://github.com/jstjohn/SeqPrep
Anyone preparing one/aware of someone preparing one? Otherwise I'll put one 
together.

 From its description: SeqPrep is a program to merge paired end Illumina reads that 
are overlapping into a single longer read. It may also just be used for its adapter 
trimming feature without doing any paired end overlap.

Cheers,

Lionel

Lionel Guy
Uppsala University
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Lionel Guy
Fålhagsleden 13, SE-75324 Uppsala | email: guy.lio...@gmail.com | mobile: +46 
(0)73 9760618 | phone: +46 (0)18 410 7398



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[galaxy-dev] SeqPrep wrapper?

2013-10-14 Thread Lionel Guy

Hi,

I'm interested in a wrapper for SeqPrep:
https://github.com/jstjohn/SeqPrep
Anyone preparing one/aware of someone preparing one? Otherwise I'll put 
one together.


From its description: SeqPrep is a program to merge paired end 
Illumina reads that are overlapping into a single longer read. It may 
also just be used for its adapter trimming feature without doing any 
paired end overlap.


Cheers,

Lionel

Lionel Guy
Uppsala University
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Re: [galaxy-dev] SeqPrep wrapper?

2013-10-14 Thread Lionel Guy
Hi Brad,

(cc-ing the list)

I'm more interested in the merging part, and after a quick search on the 
toolshed, there are no tools to merge reads. Seems that there is a need for a 
read merger wrapper then...

Lionel

On 14 Oct 2013, at 13:46 , Langhorst, Brad langho...@neb.com wrote:

 I would also like to see a seqprep wrapper… 
 if you need something sooner, cutdadapt is already wrapped and i'm pretty 
 sure there is an existing tool to merge reads as well.
 
 Brad
 --
 Brad Langhorst
 Applications and Product Development Scientist
 
 On Oct 14, 2013, at 6:59 AM, Lionel Guy guy.lio...@gmail.com
 wrote:
 
 Hi,
 
 I'm interested in a wrapper for SeqPrep:
 https://github.com/jstjohn/SeqPrep
 Anyone preparing one/aware of someone preparing one? Otherwise I'll put one 
 together.
 
 From its description: SeqPrep is a program to merge paired end Illumina 
 reads that are overlapping into a single longer read. It may also just be 
 used for its adapter trimming feature without doing any paired end overlap.
 
 Cheers,
 
 Lionel
 
 Lionel Guy
 Uppsala University
 ___
 Please keep all replies on the list by using reply all
 in your mail client.  To manage your subscriptions to this
 and other Galaxy lists, please use the interface at:
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 To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/
 

--
Lionel Guy 
Fålhagsleden 13, SE-75324 Uppsala | email: guy.lio...@gmail.com | mobile: +46 
(0)73 9760618 | phone: +46 (0)18 410 7398


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