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Discuss #2

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sjackman opened this issue Apr 24, 2018 · 2 comments
Open

Discuss #2

sjackman opened this issue Apr 24, 2018 · 2 comments
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Discuss random thoughts here.
@sjackman sjackman added the question Further information is requested label Apr 24, 2018
@sjackman sjackman self-assigned this Apr 24, 2018
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sjackman commented Apr 24, 2018 •
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assemblerflow.py assembles Nextflow pipelines of modular tools for genome assembly.
https://github.com/ODiogoSilva/assemblerflow#readme
For example

assemblerflow.py build -t "trimmomatic fastqc skesa pilon" -o my_pipeline.nf
nextflow run my_pipeline.nf --fastq path/reads.fastq

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sjackman commented Apr 24, 2018 •
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Shovill is a good example of an assembly pipeline. https://github.com/tseemann/shovill#main-steps
I wonder whether the subcomponents of SPAdes could be separated.

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