User: WilliamS

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WilliamS310
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Posts by WilliamS

<prev • 7 results • page 1 of 1 • next >
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Answer: A: From linear strings to graphs
... See also this MIT technology review article: http://www.technologyreview.com/news/537916/rebooting-the-human-genome/ This picture below  I think also gives a good overview of the idea of a string graph reference genome. Aligning reads or whole genomes to this graph would lead to a path, or a new p ...
written 4.5 years ago by WilliamS310
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Comment: C: Genomics is not Special. Computational Biologist are reinventing the wheel for b
... ## THIS IS ALL STILL EXPERIMENTAL!! ## DO NOT USE FOR PRODUCTION!! ## LOOK AT THE ROADMAP AND FEEDBACK WHAT YOU FIND IMPORTANT!! ...
written 5.4 years ago by WilliamS310
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Answer: A: Arvados vs Big Data Genomics
... I am trying Adam / Spark / BigDataGenomics for storage and retrieval / analysis on 1000 genomes VCF data. They are hoping to have a production release end of this year. Arvados looks like they are building everything from scratch https://arvados.org/projects/arvados/wiki/Technical_Architecture w ...
written 5.4 years ago by WilliamS310
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Job: Experienced lead bioinformatician at NSilico in Cork Ireland, 100K euro plus
... Bioinformatician - Marie Curie Very Experienced Researcher NSilico Life Science Ltd. is an exciting new bioinformatics company based in Cork, Ireland.  The company has made rapid progress since its inception over 2 years ago and as part of its expansion seeks to recruit an experienced bioinformati ...
job written 5.7 years ago by WilliamS310
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Comment: C: Why are we still using Bam files? And not Cram, HDF5 or improved Bam files?
... I've used the HDF Java api (which sits on top of the c api) to process HDF files without much of a problem. ...
written 5.7 years ago by WilliamS310
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Comment: C: Why are we still using Bam files? And not Cram, HDF5 or improved Bam files?
... There is a specific format and API (BioHDF) to store alignments in HDF and there is a method to import a sam file or stream. http://www.hdfgroup.org/projects/biohdf/api_docs/html/group__bioh5g__alignments.html   http://www.hdfgroup.org/projects/biohdf/api_docs/html/group__bioh5g__alignments.html  Th ...
written 5.7 years ago by WilliamS310
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Why are we still using Bam files? And not Cram, HDF5 or improved Bam files?
... The Bam format was developed at a time when io (disk / network) was not a limiting factor for genomics data analysis.  Currently it is. Especially when you have pipelines like GATK that process Bam files in multiple steps and read and write bam files for every step (instead of in memory streaming). ...
bam cram io hdf written 5.7 years ago by WilliamS310 • updated 5.6 years ago by Pavel Senin1.9k

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Popular Question 3.2 years ago, created a question with more than 1,000 views. For Experienced lead bioinformatician at NSilico in Cork Ireland, 100K euro plus
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Great Question 5.6 years ago, created a question with more than 5,000 views. For Why are we still using Bam files? And not Cram, HDF5 or improved Bam files?
Good Question 5.7 years ago, asked a question that was upvoted at least 5 times. For Why are we still using Bam files? And not Cram, HDF5 or improved Bam files?
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