User: ropolocan

gravatar for ropolocan
ropolocan510
Reputation:
510
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Trusted
Location:
Canada
Last seen:
2 weeks, 5 days ago
Joined:
3 years, 6 months ago
Email:
r***********@uleth.ca

Posts by ropolocan

<prev • 58 results • page 1 of 6 • next >
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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 5 months ago by ropolocan510
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Answer: A: Command line blast atlas
... Hi @Lee Katz. Have you found software to do this? Thanks! ...
written 8 months ago by ropolocan510
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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 8 months ago by ropolocan510
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Comment: C: Snakemake vs. Nextflow: strengths and weaknesses
... Excellent! Thanks for bringing attention to this, @steve. I will definitely try it out. ...
written 11 months ago by ropolocan510
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Answer: A: Snakemake vs. Nextflow: strengths and weaknesses
... 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 15 months ago by ropolocan510
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Comment: C: Interpretation of Kraken results
... I agree. This makes sense. Thanks, @Asaf. ...
written 15 months ago by ropolocan510
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Comment: C: Interpretation of Kraken results
... Agreed. Thanks for your answer, @Joseph Hughes. ...
written 15 months ago by ropolocan510
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Interpretation of Kraken results
... 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: ...
kraken metagenomics taxonomy classification written 15 months ago by ropolocan510 • updated 15 months ago by Joseph Hughes2.7k
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Answer: A: Determining a complete genome from contigs
... Mauve can also be an option for this. ...
written 16 months ago by ropolocan510
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Answer: A: SNP Analysis of bacterial genomes
... Hello Optimist, Some tools come to mind: **Snippy**: Might be more appropriate in this case given the number of isolates you want to analyze. https://github.com/tseemann/snippy **SNVPhyl**: might be more useful if you sequence more genomes than those two since the end goal is to produce a SNV/S ...
written 16 months ago by ropolocan510

Latest awards to ropolocan

Popular Question 3 months ago, created a question with more than 1,000 views. For BWA aln vs. mem for 100bp reads
Popular Question 3 months ago, created a question with more than 1,000 views. For Samtools sorting by read names vs. chromosomal coordinates
Popular Question 3 months ago, created a question with more than 1,000 views. For Using SPAdes for assembling mitochondrial and viral genomes
Popular Question 5 months ago, created a question with more than 1,000 views. For BWA aln vs. mem for 100bp reads
Popular Question 5 months ago, created a question with more than 1,000 views. For Parallelizing MAFFT alignment of multiple FASTA files
Popular Question 8 months ago, created a question with more than 1,000 views. For Is going back to the wet lab worth it?
Great Question 9 months ago, created a question with more than 5,000 views. For Snakemake vs. Nextflow: strengths and weaknesses
Popular Question 11 months ago, created a question with more than 1,000 views. For Is going back to the wet lab worth it?
Prophet 11 months ago, created a post with more than 20 followers. For Snakemake vs. Nextflow: strengths and weaknesses
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Snakemake vs. Nextflow: strengths and weaknesses
Popular Question 18 months ago, created a question with more than 1,000 views. For Snakemake vs. Nextflow: strengths and weaknesses
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