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Posted to user@spark.apache.org by James McCabe <ja...@oranda.com> on 2016/07/22 19:31:44 UTC

Spark, Scala, and DNA sequencing

Hi!

I hope this may be of use/interest to someone:

Spark, a Worked Example: Speeding Up DNA Sequencing

http://scala-bility.blogspot.nl/2016/07/spark-worked-example-speeding-up-dna.html 


James


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Re: Spark, Scala, and DNA sequencing

Posted by James McCabe <ja...@oranda.com>.

Thanks Ofir and Sean,

I'm aware of AMPLab's ADAM. Spark is bringing down the cost of genome 
analysis to consumer level. The potential for the future of medicine is 
exciting indeed.

I normally do Scala consulting which keeps me too busy, but recently I 
finally got some spare time to look into interesting open-source 
projects like this.

James


On 24/07/16 09:09, Sean Owen wrote:
> Also also, you may be interested in GATK, built on Spark, for genomics:
> https://github.com/broadinstitute/gatk
>
>
> On Sun, Jul 24, 2016 at 7:56 AM, Ofir Manor <of...@equalum.io> wrote:
>> Hi James,
>> BTW - if you are into analyzing DNA with Spark, you may also be interested
>> in ADAM:
>>     https://github.com/bigdatagenomics/adam
>>      http://bdgenomics.org/
>>
>> Ofir Manor
>>
>> Co-Founder & CTO | Equalum
>>
>> Mobile: +972-54-7801286 | Email: ofir.manor@equalum.io
>>
>>
>> On Fri, Jul 22, 2016 at 10:31 PM, James McCabe <ja...@oranda.com> wrote:
>>> Hi!
>>>
>>> I hope this may be of use/interest to someone:
>>>
>>> Spark, a Worked Example: Speeding Up DNA Sequencing
>>>
>>>
>>> http://scala-bility.blogspot.nl/2016/07/spark-worked-example-speeding-up-dna.html
>>>
>>> James
>>>
>>>
>>> ---------------------------------------------------------------------
>>> To unsubscribe e-mail: user-unsubscribe@spark.apache.org
>>>


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Re: Spark, Scala, and DNA sequencing

Posted by Sean Owen <so...@cloudera.com>.

Also also, you may be interested in GATK, built on Spark, for genomics:
https://github.com/broadinstitute/gatk


On Sun, Jul 24, 2016 at 7:56 AM, Ofir Manor <of...@equalum.io> wrote:
> Hi James,
> BTW - if you are into analyzing DNA with Spark, you may also be interested
> in ADAM:
>    https://github.com/bigdatagenomics/adam
>     http://bdgenomics.org/
>
> Ofir Manor
>
> Co-Founder & CTO | Equalum
>
> Mobile: +972-54-7801286 | Email: ofir.manor@equalum.io
>
>
> On Fri, Jul 22, 2016 at 10:31 PM, James McCabe <ja...@oranda.com> wrote:
>>
>> Hi!
>>
>> I hope this may be of use/interest to someone:
>>
>> Spark, a Worked Example: Speeding Up DNA Sequencing
>>
>>
>> http://scala-bility.blogspot.nl/2016/07/spark-worked-example-speeding-up-dna.html
>>
>> James
>>
>>
>> ---------------------------------------------------------------------
>> To unsubscribe e-mail: user-unsubscribe@spark.apache.org
>>
>

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Re: Spark, Scala, and DNA sequencing

Posted by Ofir Manor <of...@equalum.io>.

Hi James,
BTW - if you are into analyzing DNA with Spark, you may also be interested
in ADAM:
   https://github.com/bigdatagenomics/adam
    http://bdgenomics.org/

Ofir Manor

Co-Founder & CTO | Equalum

Mobile: +972-54-7801286 | Email: ofir.manor@equalum.io

On Fri, Jul 22, 2016 at 10:31 PM, James McCabe <ja...@oranda.com> wrote:

> Hi!
>
> I hope this may be of use/interest to someone:
>
> Spark, a Worked Example: Speeding Up DNA Sequencing
>
>
> http://scala-bility.blogspot.nl/2016/07/spark-worked-example-speeding-up-dna.html
>
> James
>
>
> ---------------------------------------------------------------------
> To unsubscribe e-mail: user-unsubscribe@spark.apache.org
>
>