User: egafni

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egafni30
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2 years, 5 months ago
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3 years, 10 months ago
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Posts by egafni

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Comment: C: How To Decide Which Software To Use For Building Automated Ngs Analysis Pipeline
... Check out https://github.com/LPM-HMS/COSMOS2 ...
written 2.5 years ago by egafni30
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Answer: A: Workflow management software for pipeline development in NGS
... Another option is [Cosmos][1], which has all of the features you mentioned. It is very stable and various groups have used it to process many thousands of genomes. The author works at a large clinical sequencing laboratory. Features include: - Written in python which is easy to learn, powerful, ...
written 2.5 years ago by egafni30
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Comment: C: Workflow management software for pipeline development in NGS
... Another python library ready for use in a production environment is [Cosmos][1]. Disclosure, I'm the author. [1]: https://github.com/LPM-HMS/COSMOS2 ...
written 2.5 years ago by egafni30
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Comment: C: Tool for random access to indexed BAM files in S3?
... Just noting here that if you have a bucket name with a "." (period) in it, samtools view will not work.  Hope that saves you the hours it took me to figure it out! ...
written 3.9 years ago by egafni30
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Comment: C: Tool for random access to indexed BAM files in S3?
... Just tried this and it worked!  Thanks! Only problem I had was: git clone https://github.com/samtools/samtools.git -b 1.2 For some unknown reason, I had to checkout the 1.2 branch manually inside the directory ...
written 3.9 years ago by egafni30

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