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tool-installation.md

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Tool Installation & Tool Execution

For all tasks use this input file: ~/genepi-teaching/ngs-bioinformatics/data/fastq/demo/miseq/5118_S39_L001_R1_001.fastq

Task 1: Install and Run Fastp

Go to https://github.com/OpenGene/fastp and install fastp using “compile from source” into your directory here: genepi-lehre/teaching/ngs-bioinformatics/students/<your-q-number>/fastp

Pick a fastq file, execute fastp and transfer report locally

Bonus Task: Execute FastQC on the new file.

Task 2: Executing Seqtk

Seqtk is a toolkit for processing sequences in FASTA/Q formats. Please use seqtk to (a) extracts reads from a fastq file (using sample) and (b) to convert a fastq file to a fasta (using seq -a).

Save your output files in genepi-lehre/teaching/ngs-bioinformatics/students/<your-q-number>/seqtk.

Task 3: Create a script

Create a for loop and execute seqtk on all files in ~/genepi-teaching/ngs-bioinformatics/data/fastq/demo/miseq/

Task 4: Have a look at https://nf-co.re/

Any pipelines available useful for your lab?