Quality control workflow

Resources

• Workshop code
• An Introduction to ShortRead (Quality control page 8)=

Quality control workflow

The ShortRead package contains a function called qa() which creates a quality report from several input formats, (usually a Fastq file). This function produces similar outputs to FastqQC executes slightly faster. Functionality has been written to perform quality control;

 # on a ShortReadQ structure which has to be loads NGS reads from a Fastq file into R using readFastq()

 Run qa()  directly from the Fastq file itself

garbageAn Introduction to ShortRead (Quality control page 8)=

Quality control workflow

The ShortRead package contains a function called qa() which creates a quality report from several input formats, (usually a Fastq file). This function produces similar outputs to FastqQC executes slightly faster. Functionality has been written to perform quality control;

 # on a '''ShortReadQ''' structure which has to be loads NGS reads from a Fastq file into R using '''readFastq()'''

 Run '''qa()'''  directly from the Fastq file itself