Gist d5a955d9a667be4ff4afe7064affbb31

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Gist d5a955d9a667be4ff4afe7064affbb31

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Last edited Feb 8, 2019

Created on Feb 8, 2019

This example demonstrates a bioinformatics mapping workflow for processing sequencing reads. The shell script uses the BWA alignment tool to map trimmed FASTQ files from multiple clones against a reference genome (NC_012967.fas). It first indexes the reference with `bwa index`, then iterates through a list of runs from `fastq/list_run`, performing alignment with `bwa aln` using four threads and converting the results to SAM format with `bwa samse` while adding read-group metadata via the `-r` flag. The script outputs aligned SAM files into the `mapping` directory.

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