FASTQC

FastQC is a quality control tool for high throughput sequencing data. It provides a quick assessment of the quality of sequencing data by analyzing FASTQ files and producing an HTML report with visualizations and summary statistics. It is widely used as an initial QC step in genomics workflows to identify problems such as poor base quality, biased nucleotide composition, or adapter contamination.

FastQC is implemented in Java and runs on major operating systems. It is distributed as a standalone application with a graphical user interface and also supports a command-line mode for integration into pipelines. The tool can read both uncompressed and gzip-compressed FASTQ files and supports common read formats used by Illumina and other platforms.

Its QC report consists of multiple modules, including basic statistics, per-base sequence quality, per-sequence quality scores, per-base sequence content, per-sequence GC content, per-base N content, sequence length distribution, duplication levels, overrepresented sequences, adapter content, and k-mer content. The output includes an interactive HTML report and downloadable data tables. It highlights warnings when metrics fall outside expected ranges.

FastQC can be used on a single sample or in batches and is often used in conjunction with other tools in workflows such as MultiQC, which aggregates reports from many samples. It has been maintained by the Babraham Institute's Bioinformatics group and has seen widespread adoption in the genomics community since its initial release.