User: brian.fristensky
brian.fristensky • 80
- Reputation:
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- Location:
- Canada/University of Manitoba
- Website:
- http://home.cc.umanito...
- Last seen:
- 1 month ago
- Joined:
- 2 years, 3 months ago
- Email:
- b***************@umanitoba.ca
Posts by brian.fristensky
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... I agree, the site uses pretty basic HTML. In fact, if I had it in the budget, I would probably do exactly that. The ToDo list is very long, and like a lot of things in bioinformatics, new features and bug fixes tend to get priority. ...
written 4 weeks ago by
brian.fristensky • 80
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... SeqKit works with both fastq and fasta files. ...
written 4 weeks ago by
brian.fristensky • 80
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... See answer at [https://www.biostars.org/p/390692/][1]
[1]: https://www.biostars.org/p/390692/ ...
written 5 weeks ago by
brian.fristensky • 80
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... For de-novo genome assembly, you may wish to try the BIRCH system, which runs many of the popular assembly steps including read quality checking, trimming, error correction, and de-novo assembly using SOAPdenovo2, Spades or ABySS, and generates reports on assembly quality using Quast. All of these s ...
written 5 weeks ago by
brian.fristensky • 80
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... A more general solution is to use by Wei Shen. [SeqKit][1] is a program that does quite a large number of convenient things with fasta/fastq files, and is efficient for big files.
Example: If I have a fasta file containing chitinase sequences and I want to extract sequences whose names contain th ...
written 5 weeks ago by
brian.fristensky • 80
• updated
5 weeks ago by
RamRS ♦ 23k
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Answer:
A: error when running blastn
... You may wish to try [BIRCH][1], a comprehensive bioinformatics package, which includes desktop tools for installing and managing local copies of BLAST, and doing BLAST searches, automated through our BioLegato applications.
BLAST is demonstrated in a recent video: BIRCH - [Desktop Bioinformatics ( ...
written 5 weeks ago by
brian.fristensky • 80
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News:
BIRCH Release 3.50
... NEW:
Introducing blreads: BioLegato GUI that makes it easy to run programs involving sequencing reads including
- read trimming, error correction and quality control
- genome assembly and quality assessment
- transcriptome assembly and quality assesment
- generation of differential expression d ...
written 5 weeks ago by
brian.fristensky • 80
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... [The BIRCH system][1] includes lots of popular tools for sequence tasks. In particular, see the [tutorials page][2] on Pairwise Similarity, as well as Multiple Sequence Alignment.
You can see BIRCH in action on our [YouTube Channel][3]
BIRCH is freely available for Linux and MacOSX.
[1]: http ...
written 5 weeks ago by
brian.fristensky • 80
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... One minor point: Error messages should identify which program is generating the message. For example, both the shell and the program might generate a message, so it should be clear which one is responsible. To illustrate from an example above:
% biotool --mask reads.fq
Error: can't load /h ...
written 2.2 years ago by
brian.fristensky • 80
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... **NEW:**
- New programs for comparative genomics
- New tutorials
- Improvements to management of local BLAST databases
**BIRCH is**
- a comprehensive desktop bioinformatics system which comes with many of the commonly-used bioinformatics programs pre-installed
- a framework of tools, files, an ...
written 2.3 years ago by
brian.fristensky • 80
Latest awards to brian.fristensky
Teacher
5 weeks ago,
created an answer with at least 3 up-votes.
For A: Extract specific genes from a FASTA file.
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