User: ropolocan
ropolocan • 270
- Reputation:
- 270
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- Canada
- Last seen:
- 3 days, 17 hours ago
- Joined:
- 2 years ago
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Posts by ropolocan
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Comment:
C: BWA aln vs. mem for 100bp reads
... Thank you so much, @genomoax! ...
written 12 weeks ago by
ropolocan • 270
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... Hello everyone,
Which BWA algorithm is a better choice for aligning 100 bp Illumina reads? BWA aln or BWA mem? I have read that BWA mem is usually faster, and more accurate, but what is BWA aln useful for then? Thanks. ...
written 12 weeks ago by
ropolocan • 270
• updated
12 weeks ago by
Pierre Lindenbaum ♦ 99k
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... Thank you very much your answer, @venu. Yes, by other approaches I meant not creating a library, but sharing R scripts and R Markdown documentation via Github instead. ...
written 4 months ago by
ropolocan • 270
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... Hello Biostars community,
Two of the things that occupy my mind the most are reproducible research and teaching skills to to others. I have been recently thinking of creating my own R package to distribute and document functions that I wrote. My goal for the immediate term is not to have the packag ...
written 4 months ago by
ropolocan • 270
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... Hello, @kamiljaron. I was not aware of BioMake; I would have to read up on it. I do not know prolog, nor have I ever used a logical programming language, but I will read more about what BioMake has to offer. ...
written 4 months ago by
ropolocan • 270
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... Thank you very much for your answer, @Sinji. I also look forward to test Nextflow. Both workflow systems/languages have so much potential. I think they could make a very important impact on bionformatics.
...
written 4 months ago by
ropolocan • 270
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... Thank you very much for your answer, @dariober.
> It seems to me that snakemake and nextflow are pretty much on a draw for all these metrics and both are pretty good (although in terms of user base and developers they are far from tools like luigi). So I think it's a difficult choice between the ...
written 4 months ago by
ropolocan • 270
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... I just read this excellent review by @Jeremy Leipzig. This article can be helpful for deciding which workflow management system is more suitable to each one's needs: https://academic.oup.com/bib/article-lookup/doi/10.1093/bib/bbw020 ...
written 4 months ago by
ropolocan • 270
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... Thanks for sharing this table, @shenwei356! It is very interesting to see that `nextflow` has stream processing, workflow versioning, and full support for SLURM, in addition to having native task support for any language. I believe `snakemake` has native task support for R now as well. Thanks again ...
written 4 months ago by
ropolocan • 270
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12 follow
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... I have seen increasing interest in workflow/pipeline management systems such as `snakemake` and `nextflow`. In my opinion, both seem very interesting and very promising. There is a very interesting review from 2016 in which `bash`, `make`, `snakemake` and `nextflow` were compared: https://www.jmazz. ...
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created a question with more than 1,000 views.
For Snakemake vs. Nextflow: strengths and weaknesses
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voted more than 100 times.
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4 months ago,
created a post with more than 5 votes.
For Snakemake vs. Nextflow: strengths and weaknesses
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