FastQC is a tool which takes a FASTQ file and runs a series of tests on it to generate a comprehensive QC report. This report will tell you if there is anything unusual about your sequence. Each test is flagged as a pass, warning, or fail depending on how far it departs from what you would expect from a normal large dataset with no significant biases. It is important to stress that warnings or even failures do not necessarily mean that there is a problem with your data, only that it is unusual. It is possible that the biological nature of your sample means that you would expect this particular bias in your results.
FastQC inputs
FASTQ file
FastQC outputs
Html report and data tables ...
App to use
FastQC CWL 1.0
Qualimap
Qualimap is an application written in Java and R that facilitates the quality control of alignment sequencing data. In short, Qualimap does the following:
Examines sequencing alignment data according to the features of the mapped reads and their genomic properties.
Provides an overall view of the data that helps detect biases in the sequencing and/or mapping of the data and eases decision-making for further analysis.
Here is the needed files:
FastQC
FastQC is a tool which takes a FASTQ file and runs a series of tests on it to generate a comprehensive QC report. This report will tell you if there is anything unusual about your sequence. Each test is flagged as a pass, warning, or fail depending on how far it departs from what you would expect from a normal large dataset with no significant biases. It is important to stress that warnings or even failures do not necessarily mean that there is a problem with your data, only that it is unusual. It is possible that the biological nature of your sample means that you would expect this particular bias in your results.
Qualimap
Qualimap is an application written in Java and R that facilitates the quality control of alignment sequencing data. In short, Qualimap does the following: