Running metassembler using latest Bowtie2 release (2.3.2)

[Charles Bridges]

Hi, I'm trying to figure out how to use a single, interleaved paired-end library in metassembler. I'm running the latest release of Bowtie2, v2.3.2 which allows the user to use a single library using the parameter --interleaved. Will metassembler pass this parameter to Bowtie2? How is this written in the metassembler config file under the [global] section? I imagine something like:

bowtie2_interleaved

Thanks for your help.

[Michael Schatz]

Thanks for your interest, but unfortunately interleaved fastq files are not
supported. Id recommend you deinterleave the fastq files using a script
like this:
https://gist.github.com/nathanhaigh/3521724

Good luck!

Mike

On Mon, May 29, 2017 at 9:22 PM, Charles Bridges cmb12@users.sf.net wrote:

Hi, I'm trying to figure out how to use a single, interleaved paired-end
library in metassembler. I'm running the latest release of Bowtie2, v2.3.2
which allows the user to use a single library using the parameter
--interleaved. Will metassembler pass this parameter to Bowtie2? How is
this written in the metassembler config file under the [global] section?
I imagine something like:

~~~
bowtie2_interleaved
~~~

Thanks for your help.

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Running metassembler using latest Bowtie2 release (2.3.2)

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