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Search: Posts Made By: Shini Sunagawa
Forum: Academic/Non-Profit Jobs 10-04-2017, 11:32 PM
Replies: 0
Views: 362
Posted By Shini Sunagawa
Staff Bioinformatician/Computational Biologist, Institute of [email protected] Zurich

Direct link:
https://www.ethz.ch/content/dam/ethz/special-interest/biol/micro-biol/inst-of-microbiology-dam/documents/positions/SS%20Open%20Positions/Staff_Bioinf_position.pdf

Description:
The...
Forum: Academic/Non-Profit Jobs 01-14-2017, 01:21 AM
Replies: 1
Views: 1,160
Posted By Shini Sunagawa
Job post updated

Please note that the job description above has been updated.
Best regards,
Shini Sunagawa
Forum: Bioinformatics 09-27-2016, 04:13 AM
Replies: 636
Views: 121,946
Posted By Shini Sunagawa
Hi Brian, This sounds really great! ...

Hi Brian,

This sounds really great!

Just FYI, I ran another large clustering job in less then 5 h, which required >1 month (!) using alternative tools, with similar output. As I said, it is...
Forum: Academic/Non-Profit Jobs 09-22-2016, 05:01 AM
Replies: 1
Views: 1,160
Posted By Shini Sunagawa
Bioinformatician/Computational Biologist in Microbiome Research @ETH Zurich

Direct link to pdf:
http://sunagawalab.ethz.ch/jobs/BioinfCompBio.position.ETHZ.pdf

Description:
We are seeking a highly motivated, skilled and organized bioinformatician/computational biologist...
Forum: Bioinformatics 09-22-2016, 02:51 AM
Replies: 636
Views: 121,946
Posted By Shini Sunagawa
Hi Brian, Since I saw increased activity...

Hi Brian,

Since I saw increased activity lately again, I was wondering if you might have thought about the issue we discussed back in January (~post #300). It was about dedupe not writing out...
Forum: Bioinformatics 01-30-2016, 01:19 AM
Replies: 636
Views: 121,946
Posted By Shini Sunagawa
Just to make sure we are on the same page, I...

Just to make sure we are on the same page, I attach the toy input file I described earlier.

Running:

dedupe.sh in=in.fa out=out.fa outd=outd.fa am=t ac=t fo=f dot=dot.txt

will give the...
Forum: Bioinformatics 01-29-2016, 04:09 AM
Replies: 636
Views: 121,946
Posted By Shini Sunagawa
Hi Brian, Thanks for you quick response,...

Hi Brian,

Thanks for you quick response, really appreciate you took some of your limited time!

I hoped the dot file might be just what I was looking for, so I ran

dedupe.sh in=in.fa...
Forum: Bioinformatics 01-27-2016, 11:58 PM
Replies: 636
Views: 121,946
Posted By Shini Sunagawa
dedupe.sh

Dear Brian,

I have been looking for a tool that would quickly dereplicate (100% containments) nucleotide sequences and track for each unique sequence the identifiers of the removed duplicates.
...
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