SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 13 of 13
Search took 0.00 seconds.
Search: Posts Made By: jvhaarst
Forum: Bioinformatics 04-20-2011, 11:14 AM
Replies: 2
Views: 2,741
Posted By jvhaarst
It has been a while since I looked at SOAPdenovo,...

It has been a while since I looked at SOAPdenovo, but could you try this config ?
----
#maximal read length
max_rd_len=100
[LIB]
#average insert size
avg_ins=200
#if sequence needs to be...
Forum: 454 Pyrosequencing 02-08-2011, 05:04 AM
Replies: 30
Views: 22,026
Posted By jvhaarst
I have done a quick analysis of the basecalling...

I have done a quick analysis of the basecalling differences between 2.3 and 2.5.3:
https://dl.dropbox.com/s/z6fxnqamsrcaayi/2.3%20vs%202.5.3.png?dl=1

The higher resolution pdf (with summary...
Forum: 454 Pyrosequencing 01-24-2011, 03:21 AM
Replies: 30
Views: 22,026
Posted By jvhaarst
The Data Processing rpm's can be 'installed' ...

The Data Processing rpm's can be 'installed' like this:

First download the DataProcessing_2.5.3.tgz file.
Extract that file in a place of your liking.

In a terminal, go to the directory...
Forum: Bioinformatics 04-12-2010, 11:09 PM
Replies: 10
Views: 4,207
Posted By jvhaarst
Curtain

You could give Curtain (http://seqanswers.com/wiki/Curtain) a try.
From the wiki:
Curtain is a Java wrapper around next-generation assemblers such as Velvet which allows the incremental...
Forum: 454 Pyrosequencing 09-08-2009, 06:03 AM
Replies: 9
Views: 3,456
Posted By jvhaarst
For now, I think I will first have a test with...

For now, I think I will first have a test with the changed reads.
I myself wouldn't change the start of the reads, because that would make it harder to see which run produced a read. This means that...
Forum: 454 Pyrosequencing 09-08-2009, 03:12 AM
Replies: 9
Views: 3,456
Posted By jvhaarst
Great ! This saves me (and probably others) a...

Great !
This saves me (and probably others) a lot of time.
Adding the index and the manifest shouldn't be that hard, would it ?
The index is probably just a sorted list with IDs, and an adress ?
Forum: 454 Pyrosequencing 09-08-2009, 01:43 AM
Replies: 9
Views: 3,456
Posted By jvhaarst
I don't care about the index, one could...

I don't care about the index, one could reconstruct that easily with sfffile.
I just had a look at iolib and sff_extract, and they both don't have information about the manifest.
I can see that it...
Forum: 454 Pyrosequencing 09-06-2009, 11:48 PM
Replies: 9
Views: 3,456
Posted By jvhaarst
Yes, that would be very helpful. Would it be OK...

Yes, that would be very helpful.
Would it be OK if I published it on a website somewhere if it works satisfactory ?
Forum: 454 Pyrosequencing 09-04-2009, 01:15 AM
Replies: 9
Views: 3,456
Posted By jvhaarst
Lightbulb Renaming reads within SFF files

Hello,
Has anybody a script/software to rename reads within an SFF file ?
We are getting data back from providers that have been tagged/barcoded .
We can split the data without a problem, but it...
Forum: De novo discovery 05-18-2009, 12:41 AM
Replies: 3
Views: 2,880
Posted By jvhaarst
I'm in the process of doing just that (1GB genome...

I'm in the process of doing just that (1GB genome done with Illumina data), I'll post my results.
I'll first have a go with SOAPdenovo, see where that leads me.
Forum: 454 Pyrosequencing 05-04-2009, 05:32 AM
Replies: 2
Views: 2,174
Posted By jvhaarst
In short : You can't. We had Newbler...

In short : You can't.

We had Newbler throwing away 50% of the reads, so we had a look at CABOG, which in our case looks to be the better choice.
Forum: Academic/Non-Profit Jobs 02-25-2009, 01:59 AM
Replies: 1
Views: 5,033
Posted By jvhaarst
Exclamation Date extended to March 16 !

Dear possible applicant,

The date for entry has been extended to March 16.

With kind regards,
Jan
Forum: Academic/Non-Profit Jobs 02-06-2009, 03:45 AM
Replies: 1
Views: 5,033
Posted By jvhaarst
Postdoc Plant Genome Assembly , Wageningen (The Netherlands)

Postdoc Plant Genome Assembly


Laboratory of Bioinformatics of Wageningen University and Research Centre
Wageningen (The Netherlands), 38 hours per week
Reference number: DPW 09-10
...
Showing results 1 to 13 of 13

 


All times are GMT -8. The time now is 03:05 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO