Re: [galaxy-dev] SeqPrep wrapper?
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" 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 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: http://lists.bx.psu.edu/ 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 ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] SeqPrep wrapper?
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" 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 > 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: >> http://lists.bx.psu.edu/ >> >> 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 ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] SeqPrep wrapper?
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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
