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Forum: Bioinformatics 09-20-2011, 08:31 AM
Replies: 1
Views: 1,829
Posted By pierre350d
The libjudy location should be present in your...

The libjudy location should be present in your "$LD_LIBRARY_PATH" and not only in your "$PATH".
You may overcome this problem with the following command: export...
Forum: De novo discovery 09-12-2011, 07:58 AM
Replies: 8
Views: 5,183
Posted By pierre350d
Dear salmonella, Sorry for this late...

Dear salmonella,

Sorry for this late answer...

I'm one of the authors of Mapsembler.
The output of mapsembler, while used using the graph output, can be viewed by any viewer able to deal with...
Forum: De novo discovery 06-21-2011, 12:10 AM
Replies: 8
Views: 5,183
Posted By pierre350d
Dear all, I'd like to mention a tool called...

Dear all,

I'd like to mention a tool called mapsembler. It takes some sequence fragments and a set of (illumina) reads. It tries to reconstruct each sequence fragment using the reads (authorizing...
Forum: De novo discovery 03-30-2011, 12:23 PM
Replies: 5
Views: 4,862
Posted By pierre350d
Thanks for the link. I take the opportunity...

Thanks for the link.

I take the opportunity of this "up" to inform you that a new version of kisSnp is available: http://alcovna.genouest.org/kissnp-page/

Pierre
Forum: De novo discovery 02-07-2011, 01:28 AM
Replies: 5
Views: 4,862
Posted By pierre350d
Dear Marius, At INRIA, France we developped...

Dear Marius,

At INRIA, France we developped an algorithm, called kisSnp that compares two sets of raw reads. It detects from these sets SNP polymorphism.

We have a public validated Java...
Forum: De novo discovery 09-29-2010, 08:07 AM
Replies: 38
Views: 17,077
Posted By pierre350d
With the current version we detect only SNPs...

With the current version we detect only SNPs between individuals. One compares two set of reads, focusing on small substitutions that may be those SNPs.

We are currently working on a version...
Forum: De novo discovery 09-29-2010, 12:38 AM
Replies: 38
Views: 17,077
Posted By pierre350d
A piece of information, We developed a...

A piece of information,

We developed a tool, called kisSnp that takes two sets of non assembled raw short reads and compare them for finding SNPs between these two sets.
It outputs the SNPs...
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