User: ropolocan
ropolocan • 680
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- Canada
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- 1 year, 4 months ago
- Joined:
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Posts by ropolocan
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... Hello,
Does anyone have experience importing pyrosequencing data into QIIME2? I am aware that there is a plugin to denoise pyrosequencing data (https://docs.qiime2.org/2019.1/plugins/available/dada2/denoise-pyro/ ), but I am struggling trying to import the data as a QIIME2 artifact. Any guidance wo ...
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Answer:
A: Reference based assembly
... There are other approaches that I might suggest instead of mapping reads to a reference genome. You can start with *de novo* assembly, and then scaffold your assembly with the help of a reference genome. For example, [ragout](http://fenderglass.github.io/Ragout/usage.html) does use reference genomes ...
written 22 months ago by
ropolocan • 680
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Answer:
A: Command line blast atlas
... Hi @Lee Katz. Have you found software to do this? Thanks! ...
written 2.1 years ago by
ropolocan • 680
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Comment:
C: GFA to Fasta file
... GFA is the Graphical Fragment Assembly format. Here is a post by Heng Li (@lh3) on this: https://lh3.github.io/2014/07/19/a-proposal-of-the-grapical-fragment-assembly-format. ...
written 2.1 years ago by
ropolocan • 680
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... Excellent! Thanks for bringing attention to this, @steve. I will definitely try it out. ...
written 2.3 years ago by
ropolocan • 680
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... I thought I would share this Reddit thread on workflow management systems. There are very interesting posts on `snakemake` vs. `nextflow`: https://www.reddit.com/r/bioinformatics/comments/73am0k/ncbi_hackathons_discussions_on_bioinformatics/ ...
written 2.7 years ago by
ropolocan • 680
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Comment:
C: Interpretation of Kraken results
... I agree. This makes sense. Thanks, @Asaf. ...
written 2.7 years ago by
ropolocan • 680
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Comment:
C: Interpretation of Kraken results
... Agreed. Thanks for your answer, @Joseph Hughes. ...
written 2.7 years ago by
ropolocan • 680
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... Dear Biostars community:
I have been using Kraken extensively for the characterization of microbiomes. My colleague and I have a bit of a disagreement on how to interpret the results from the Kraken reports.
For example, let’s imagine we have a subset of a Kraken report that looks like this:
...
written 2.7 years ago by
ropolocan • 680
• updated
2.7 years ago by
Joseph Hughes • 2.8k
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... Mauve can also be an option for this. ...
written 2.8 years ago by
ropolocan • 680
Latest awards to ropolocan
Epic Question
17 months ago,
created a question with more than 10,000 views.
For Snakemake vs. Nextflow: strengths and weaknesses
Popular Question
21 months ago,
created a question with more than 1,000 views.
For BWA aln vs. mem for 100bp reads
Popular Question
21 months ago,
created a question with more than 1,000 views.
For Samtools sorting by read names vs. chromosomal coordinates
Popular Question
21 months ago,
created a question with more than 1,000 views.
For Using SPAdes for assembling mitochondrial and viral genomes
Popular Question
22 months ago,
created a question with more than 1,000 views.
For BWA aln vs. mem for 100bp reads
Popular Question
22 months ago,
created a question with more than 1,000 views.
For Parallelizing MAFFT alignment of multiple FASTA files
Popular Question
2.1 years ago,
created a question with more than 1,000 views.
For Is going back to the wet lab worth it?
Great Question
2.2 years ago,
created a question with more than 5,000 views.
For Snakemake vs. Nextflow: strengths and weaknesses
Popular Question
2.3 years ago,
created a question with more than 1,000 views.
For Is going back to the wet lab worth it?
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2.4 years ago,
created a post with more than 20 followers.
For Snakemake vs. Nextflow: strengths and weaknesses
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2.7 years ago,
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For A: Snakemake vs. Nextflow: strengths and weaknesses
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2.9 years ago,
created a question with more than 1,000 views.
For Snakemake vs. Nextflow: strengths and weaknesses
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For Snakemake vs. Nextflow: strengths and weaknesses
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For Snakemake vs. Nextflow: strengths and weaknesses
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