User: lexnederbragt

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lexnederbragt1.2k
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Oslo, Norway
Website:
http://flxlex.flavors.me/
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2 months, 2 weeks ago
Joined:
7 years, 4 months ago
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l*************@bio.uio.no

Posts by lexnederbragt

<prev • 88 results • page 1 of 9 • next >
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Answer: A: Is Newbler still available for download
... A copy of Newbler had to be requested from Roche/454 by submitting a form. However, that form is no longer available. The original URL was http://454.com/contact-us/software-request.asp, it is now dead (as is 454.com). I find this irresponsible behavior from the company. You could try to contact Ro ...
written 3 months ago by lexnederbragt1.2k
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Answer: A: Getting reads contributing to a velvet assembly - contig
... if you use the ` -amos_file yes` flag for velvetg, you'll get an `afg` file which contains this information. The viewer [Tablet][1] can be used to inspect the results. There may be suitable parsers/converters for the `afg` file that help you get what you need. [1]: https://ics.hutton.ac.uk/table ...
written 10 months ago by lexnederbragt1.2k
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Answer: A: Evaluation of PacBio only de novo assembly
... There is not a dedicated tool to do this. What comes to mind is mapping the reads back to the assembly and calling variants, especially structural variants. Tools like PBHoney, Sniffles and the like. The problem is that only looking at one assembly won't tell you much - some structural variants may ...
written 12 months ago by lexnederbragt1.2k
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Answer: A: Cleaning FASTQ files containing a contamination sequence.
... I recently discovered AdapterRemoval https://github.com/MikkelSchubert/adapterremoval, give it a try. ...
written 13 months ago by lexnederbragt1.2k
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Answer: A: Newbler 3 assembler download - assembly of highly heterozygous genome
... Have you tried using http://454.com/contact-us/software-request.asp again? That should now give you version 3.0. ...
written 14 months ago by lexnederbragt1.2k
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Comment: C: New Fasta Sequence From Reference Fasta And Variant Calls File?
... And again: https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_fasta_FastaAlternateReferenceMaker.php ...
written 20 months ago by lexnederbragt1.2k
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Comment: C: How to check whether a genome is circular
... That information is a bit outdated by now. See my answer below. ...
written 23 months ago by lexnederbragt1.2k
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Answer: A: How to check whether a genome is circular
... Have a look here: https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/Circularizing-and-trimming. Another tool that I tried and that seems to be working is Circlator http://sanger-pathogens.github.io/circlator/, but I haven't tested it extensively. ...
written 23 months ago by lexnederbragt1.2k
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Answer: A: alternative to quiver
... To my knowledge, there is no alternative.. ...
written 23 months ago by lexnederbragt1.2k
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Answer: A: Tool for PacBio Denovo assembly of diploid plant genome (size 500mb) having aro
... See my answer to a similar question here: https://www.biostars.org/p/158387/#158456. ...
written 2.1 years ago by lexnederbragt1.2k

Latest awards to lexnederbragt

Commentator 12 months ago, created a comment with at least 3 up-votes. For C: New Fasta Sequence From Reference Fasta And Variant Calls File?
Scholar 19 months ago, created an answer that has been accepted. For A: De Novo Genome Assembler Preferring Shorter Error-Free Contigs
Good Answer 20 months ago, created an answer that was upvoted at least 5 times. For A: What Does Agp Stand For?
Appreciated 20 months ago, created a post with more than 5 votes. For A: What Does Agp Stand For?
Scholar 2.4 years ago, created an answer that has been accepted. For A: De Novo Genome Assembler Preferring Shorter Error-Free Contigs
Good Answer 2.9 years ago, created an answer that was upvoted at least 5 times. For A: What Does Agp Stand For?
Appreciated 2.9 years ago, created a post with more than 5 votes. For A: What Does Agp Stand For?
Guru 2.9 years ago, received more than 100 upvotes.
Scholar 3.1 years ago, created an answer that has been accepted. For A: De Novo Genome Assembler Preferring Shorter Error-Free Contigs
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: How Many Contigs Is "Normal"? Newbler/454 Bacterial Genome
Appreciated 3.5 years ago, created a post with more than 5 votes. For A: What Does Agp Stand For?
Good Answer 3.5 years ago, created an answer that was upvoted at least 5 times. For A: What Does Agp Stand For?
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: What Does Agp Stand For?
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Quality Scores 454
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Circular Genome??
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Simulate Sff File
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Where Do I Find The 16S Rdna Reference Sequences (Metagenomics)
Supporter 3.5 years ago, voted at least 25 times.
Appreciated 6.6 years ago, created a post with more than 5 votes. For A: Circular Genome??
Good Answer 6.6 years ago, created an answer that was upvoted at least 5 times. For A: Circular Genome??
Teacher 7.1 years ago, created an answer with at least 3 up-votes. For A: Where Do I Find The 16S Rdna Reference Sequences (Metagenomics)
Good Answer 7.3 years ago, created an answer that was upvoted at least 5 times. For A: Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
Teacher 7.3 years ago, created an answer with at least 3 up-votes. For A: Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
Good Answer 7.4 years ago, created an answer that was upvoted at least 5 times. For A: Order Sequences By Number Of Times Found

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