FastQC

Perform QC from your reads prior to other NGS processing

suggests : cutadapt, seq_crumbs, PrinSeq, FastX_toolkit

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FastQC()) aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis (watch the tutorial video here).

FastQC is a very popular standalone Java GUI application running on all platforms.

FastQC also runs as a command line to submit runs in batch and store the html reports as zip files for later review (see: Perform basic read QC at command line prior to mapping)

The main functions of FastQC are:

• Import of data from BAM, SAM or FastQ files (any variant)
• Providing a quick overview to tell you in which areas there may be problems
• Summary graphs and tables to quickly assess your data
• Export of results to an HTML based permanent report
• Offline operation to allow automated generation of reports without running the interactive application

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References:

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