This is the Linux app named Just_Preprocess_My_Reads whose latest release can be downloaded as justpreprocessmyreads_Aug2015c.tar.gz. It can be run online in the free hosting provider OnWorks for workstations.
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Identifies rRNA, contaminants, trims in a standard fashion etc. Maintains read pairs. Built for fire-and-forget high throughput projects (terabytes of data).
Uses pbzip2, bowtie2, fastx_toolkit, samtools, fastqc, Trimmomatic (optional)
- illumina pre-processing
- contamination checking
This is an application that can also be fetched from https://sourceforge.net/projects/justpreprocessmyreads/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.