User: ropolocan
ropolocan • 510
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Posts by ropolocan
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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
ropolocan • 510
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A: Command line blast atlas
... Hi @Lee Katz. Have you found software to do this? Thanks! ...
written 8 months ago by
ropolocan • 510
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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
ropolocan • 510
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... Excellent! Thanks for bringing attention to this, @steve. I will definitely try it out. ...
written 11 months ago by
ropolocan • 510
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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 15 months ago by
ropolocan • 510
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C: Interpretation of Kraken results
... I agree. This makes sense. Thanks, @Asaf. ...
written 15 months ago by
ropolocan • 510
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C: Interpretation of Kraken results
... Agreed. Thanks for your answer, @Joseph Hughes. ...
written 15 months ago by
ropolocan • 510
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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 15 months ago by
ropolocan • 510
• updated
15 months ago by
Joseph Hughes • 2.7k
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... Mauve can also be an option for this. ...
written 16 months ago by
ropolocan • 510
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... 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
ropolocan • 510
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