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Search: Posts Made By: TauOvermind
Forum: Bioinformatics 11-17-2015, 10:28 AM
Replies: 2
Views: 1,288
Posted By TauOvermind
Thank you, Brian. I agree that the difference...

Thank you, Brian. I agree that the difference between these two values would be minimal in practice, but as it was a paper about the theory of sequence assembly, I found that statement confusing, as...
Forum: Bioinformatics 11-15-2015, 05:23 AM
Replies: 2
Views: 1,288
Posted By TauOvermind
Minimal overlap between two reads in the de Bruijn algorithm

I was reading a paper named "Comparison of the two major classes of assembly algorithms: overlap–layout–consensus and de-bruijn-graph" by Zhenyu Li et al. (2011)...
Forum: Bioinformatics 01-14-2015, 06:03 AM
Replies: 2
Views: 1,148
Posted By TauOvermind
rhinoceros, I completely agree with your point....

rhinoceros, I completely agree with your point. Although I spent 3 days last time waiting for IDBA-UD to finish running, I got quite good contigs in the end.
I just wanted to know if there is a way...
Forum: Bioinformatics 01-14-2015, 05:23 AM
Replies: 2
Views: 1,148
Posted By TauOvermind
Which metagenome assemblers are capable of efficient running on clusters?

Hi, I am trying to choose a metagenome assembler that would be able to run efficiently on a cluster (utilising cores from different nodes and using shared memory). While there are many very good...
Forum: Bioinformatics 01-11-2015, 04:45 PM
Replies: 10
Views: 3,612
Posted By TauOvermind
Thank you very much for both your explanations...

Thank you very much for both your explanations and the links you provided, GenoMax. I have spent a lot of time googling for a good example of a BLAST+ script for a cluster with Torque/PBS today, but...
Forum: Bioinformatics 01-11-2015, 03:57 PM
Replies: 10
Views: 3,612
Posted By TauOvermind
Thank you for your suggestions as well, GenoMax....

Thank you for your suggestions as well, GenoMax. I made a script (virulence.sh) for Torque, which would submit 6 jobs of blastx with 4 threads per each node (total 24 threads):


#!/bin/bash

...
Forum: Bioinformatics 01-11-2015, 06:19 AM
Replies: 10
Views: 3,612
Posted By TauOvermind
Thank you for clarification, and you are probably...

Thank you for clarification, and you are probably right about the jobs limit, but I am not really sure about that. I was told that I can use 48 threads per job at most, so all the rest are just my...
Forum: Bioinformatics 01-11-2015, 05:53 AM
Replies: 10
Views: 3,612
Posted By TauOvermind
maubp, thank you for your suggestion, I will try...

maubp, thank you for your suggestion, I will try it tomorrow.

Just wanted to clarify, when you mentioned two BLAST jobs running at the same time, did you mean that they would be running on the...
Forum: Bioinformatics 01-10-2015, 12:42 PM
Replies: 10
Views: 3,612
Posted By TauOvermind
Running Blast+ on multiple nodes on a cluster -- what is the best way to that?

Hi, I have been recently granted access to the HPC cluster of my university. I am going to run several blastx searches (Blast+ version, not legacy blast) there to identify potential virulence factors...
Forum: Bioinformatics 10-02-2014, 08:01 AM
Replies: 7
Views: 3,279
Posted By TauOvermind
Thank you, Brian, I updated to the latest version...

Thank you, Brian, I updated to the latest version and everything works perfectly now.
Forum: Bioinformatics 10-02-2014, 07:39 AM
Replies: 7
Views: 3,279
Posted By TauOvermind
EDIT: Sorry, it seems that problem disappeared...

EDIT: Sorry, it seems that problem disappeared after updating to BBtools v33.54.

Brian, may I ask for your help once again? I am getting these strange errors when I run dedupe.sh (I use BBtools...
Forum: Bioinformatics 10-01-2014, 02:31 PM
Replies: 7
Views: 3,279
Posted By TauOvermind
Thank you, Brian, everything is clear now. Good...

Thank you, Brian, everything is clear now. Good luck with the paper!
Forum: Bioinformatics 10-01-2014, 02:05 PM
Replies: 7
Views: 3,279
Posted By TauOvermind
Brian, thank you very much for your comprehensive...

Brian, thank you very much for your comprehensive answers and also for your BBtools package, it is very good and allows to do almost anything with NGS data.

Thank you for your advice regarding...
Forum: Bioinformatics 10-01-2014, 11:10 AM
Replies: 7
Views: 3,279
Posted By TauOvermind
Illumina PE reads optimal pre-processing sequence

Hello, everyone. I am trying to establish an optimal sequence of Illumina PE reads pre-processing steps and I have come up with the following protocol so far (the best tool for the step, in my...
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