Short-read quality control and cleanup tools
While some tools can deal rather well with reads of mixed qualities and contaminations, other will be biased and will produce incorrect results. As always in NGS data analysis, continuous and extensive quality control of the data at each step will prevent bias effects, allow comparison of your results with gold standards, and ensure that you do not perform useless and lengthy runs with 'bad' quality data.
A number of tools allow controlling NGS data at different levels. Some are presented below that show some levels of redundancy but also unique features.
- cutadapt filters out reads that contain a provided adapter (taken from FastQC reports)
- fastQC analyse reads and find biases
- fastX_toolkit cleans reads and counts read metrics
- PrinSeq, analyze and clean your reads
- Qualimap, plot mapping result QC and identify biases.
- RSeQC, perform various QC analyses on bam files obtained after read mapping (and more).
- seq_crumbs, perform various filtering on reads, including identification of the read Phred scale.
- trimmomatic for the trimming and cleaning of Illlumina reads.
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