User: Roxane Boyer

gravatar for Roxane Boyer
Roxane Boyer670
Reputation:
670
Status:
Trusted
Location:
France / Toulouse / GeT-Plage
Last seen:
an hour ago
Joined:
2 years ago
Email:
r*************@gmail.com

Recently started to work on the Toulouse sequencing platforme GeT-Plage, attached to the French National Institute of Agronomic Research (INRA). I'll most be dealing with Oxford Nanopore generated data.

Posts by Roxane Boyer

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Comment: C: Looking for a tool like fastq screen but for ONT data
... Yeah I did not specified and as I said, it was a good suggestions anyway because I did not knew the tool :) I'm surveying all the tools to think about a nice approach and I'll keep that one in mind for sure. The thing is that I don't really know yet what are my sequences of interest... Have to put m ...
written 4 hours ago by Roxane Boyer670
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Comment: C: Looking for a tool like fastq screen but for ONT data
... That was a nice suggestion, but I feel like it won't be suited for my purpose as it's a metagenomic oriented tool that will only perform for bacterial DNA right ..? ...
written 4 hours ago by Roxane Boyer670
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Comment: C: Polish PacBio assembly with latest PacBio tools : an affordable solution for eve
... Hello Vijay ! As I wrote that post almost one year ago, I'm pretty sure that the PacBio command lines for arrow and quiver changed already... Also, sadly, I had to use quiver instead of arrow in the end because I had an error even using the safe install I described. That error was only when using ar ...
written 4 hours ago by Roxane Boyer670
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Comment: C: Looking for a tool like fastq screen but for ONT data
... Who doesn't ;) I'll keep you updated when I'll try something then ! ...
written 1 day ago by Roxane Boyer670
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Comment: C: Looking for a tool like fastq screen but for ONT data
... Was thinking with python as well, as the main goal is to integrate this analysis into an existing python workflow that seemed to be the easiest solution indeed. Even better if there is an API. Thanks for the reference of NanoLyse, I'll have a look :) ...
written 1 day ago by Roxane Boyer670
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Comment: C: Looking for a tool like fastq screen but for ONT data
... I may give a try to that task myself Here is a "good luck" upvote for your thesis :) ...
written 1 day ago by Roxane Boyer670
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Comment: C: Looking for a tool like fastq screen but for ONT data
... From the NanoPlot author :o) ...
written 1 day ago by Roxane Boyer670
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Comment: C: Looking for a tool like fastq screen but for ONT data
... I'm not looking for a particular contaminant, indeed it's more like a survey of my reads content. Minimap and miniasm seems indeed interesting thanks ! ...
written 1 day ago by Roxane Boyer670
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Comment: C: Looking for a tool like fastq screen but for ONT data
... From what I understand from NanoPlot, it doesn't seems it will help me to answer to the "What did I have sequenced" question. I was more looking for a tool or a method that can determinate what organisme the reads originate from, which will both check for contamination and genome characterization (l ...
written 1 day ago by Roxane Boyer670
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Looking for a tool like fastq screen but for ONT data
... Hello Biostars ! I am currently looking for a tool similar to fastq screen : https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/fastq_screen_documentation.html , which is able to roughly characterize genome composition (did we sequenced the right species ? do we have contamination in o ...
ont minion tool nanopore gridion written 1 day ago by Roxane Boyer670 • updated 1 day ago by jrj.healey4.9k

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Popular Question 2 days ago, created a question with more than 1,000 views. For First time using maker
Scholar 6 days ago, created an answer that has been accepted. For A: Polishing PacBio assembly : The ideal coverage for higly polymorphic species
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Popular Question 5 months ago, created a question with more than 1,000 views. For First time using maker
Popular Question 5 months ago, created a question with more than 1,000 views. For What are the ".bax.h5" files generated by PacBio long reads sequencing ?
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