PE Assembler

[ewalt98]

Hi All,

Have any of you tried the PE Assembler for DeNovo yet? It sounds promising, if you read the author's paper, however, I have not been able to get to run past the second of seven steps. I've emailed the author, but have yet to hear back, so I thought I'd pose a question to the group.

If you have used it, what do you think of it, and did you encounter any issues running it?

http://seqanswers.com/wiki/PE-Assembler

Thanks in advance.

Eric

[bbsunchen]

Hi All,

Have any of you tried the PE Assembler for DeNovo yet? It sounds promising, if you read the author's paper, however, I have not been able to get to run past the second of seven steps. I've emailed the author, but have yet to hear back, so I thought I'd pose a question to the group.

If you have used it, what do you think of it, and did you encounter any issues running it?

http://seqanswers.com/wiki/PE-Assembler

Thanks in advance.

Eric

I'v tried the PE assembler for a de novo assembling of a bacteria.
I meet an error in the first step:

nPETs: 36681426
memory allocated for hashentries: 6716mb
Segmentation fault

I also try the sample data offered by PE Assembler, the first step is ok with memory allocated for hashentries about several hundred mb.
So I think the error may caused by the large memory, but I'm not sure. You know, the genome of a bacteria is very small.

I still have question of the second step about how to make a graph by the data. The "Read Me" is so simple without any error conduction.

[ewalt98]

I still have question of the second step about how to make a graph by the data. The "Read Me" is so simple without any error conduction.

Yep, it is. I've emailed the authors and am waiting to hear back from them. Will post an update if I do.