Gist 9a3defa4596db38a11fc0ec9549b4834

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Gist 9a3defa4596db38a11fc0ec9549b4834

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Last edited Feb 8, 2019

Created on Feb 8, 2019

This example demonstrates a preprocessing workflow for raw paired-end Illumina sequencing data. It shows the trimming of low-quality bases and removal of adapter sequences using the `fastq-mcf` tool from the ea-utils suite, followed by quality control reporting with `FastQC`. The script runs `fastq-mcf` with parameters for a minimum quality score of 20, a mean quality threshold, and a 150-base pair read length, producing trimmed FASTQ files. These outputs are then processed by `FastQC` to generate quality assessment reports for both the forward and reverse reads, illustrating a standard bioinformatics pipeline for high-throughput sequence data preparation.

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