fastqc_toolshed

fastqc_toolshed performs quality control assessment of raw next-generation sequencing data by calculating and reporting metrics such as per-base sequence quality, per-sequence quality scores, per-base sequence content, GC content distribution, adapter contamination, and sequence duplication levels.

Key Features:

• Quality Control Reports: Produces detailed reports that include per-base sequence quality, per-sequence quality scores, per-base sequence content, GC content distribution, adapter contamination detection, and sequence duplication metrics.
• Long Reads Compatibility: Includes options to process long-read sequencing technologies and evaluate metrics relevant to long-read datasets.
• Integration with Galaxy Project: Operates within the Galaxy framework to be incorporated into Galaxy workflows and histories for data provenance.
• Automated Tracking and Reproducibility: Records executions and outputs in Galaxy histories to enable provenance tracking and reproducible analyses.

Scientific Applications:

• Sequencing Quality Control: Identifies sequencing issues to guide data filtering and inform downstream analyses such as variant calling and genome assembly.
• Clinical and Diagnostic Sequencing: Flags contamination and low-quality regions to support quality assessment of sequencing data used in clinical contexts.
• Long-Read Genomics: Evaluates long-read datasets that span complex genomic regions to assess their suitability for downstream processing.

Methodology:

Computes statistical per-base and per-sequence metrics and generates visualizations using computational algorithms to detect adapter contamination and sequence duplications.