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.fastq Alignment #1723

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Rokshan2016 opened this Issue Sep 14, 2017 · 2 comments

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@Rokshan2016

Rokshan2016 commented Sep 14, 2017

Hi,
Is there any Adam command I can use to do .fastq / sequence alignment .

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heuermh Sep 14, 2017

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To clarify, you have unaligned sequencing reads in FASTQ format and want to align them against a reference genome assembly?

If so, my recommendation would be to run BWA on Spark via Cannoli
https://github.com/bigdatagenomics/cannoli

A workflow written in Toil can be found here
https://github.com/bigdatagenomics/workflows/blob/master/bdgenomics/workflows/cannoli_pipeline/bwa_alignment.py

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heuermh commented Sep 14, 2017

To clarify, you have unaligned sequencing reads in FASTQ format and want to align them against a reference genome assembly?

If so, my recommendation would be to run BWA on Spark via Cannoli
https://github.com/bigdatagenomics/cannoli

A workflow written in Toil can be found here
https://github.com/bigdatagenomics/workflows/blob/master/bdgenomics/workflows/cannoli_pipeline/bwa_alignment.py

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Rokshan2016 Sep 14, 2017

ok, let me try this

Thanks!

Rokshan2016 commented Sep 14, 2017

ok, let me try this

Thanks!

@heuermh heuermh added this to the 0.23.0 milestone Dec 7, 2017

@heuermh heuermh added this to Completed in Release 0.23.0 Jan 4, 2018

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