which one is a suitable tool to check the quality of NGS high throughput sequence; FastQC or MultiQC or any other tool ?
FastQC will will process one sample at a time and give you an output report for each sample separately. MultiQC will combine all the outputs from FastQC analysis and give you one QC report for all processed samples, making them more easily comparable.
Iva is right,
also sites like Biostars.org
is a good resource for these kinds of discussions as well as suggestions for other tools that people have tested out to do similar jobs, especially if you are working with command line
.
For example,
https://www.biostars.org/p/322842/
SeqAnswers is a similar resource.
use FastQC R package, you will analyse each sample and after that you can make a common report to compare them easily.
Iva is right. Just to add some, it is linux based (although there is fastqcr R package that integrated FastQC for R but MultiQC is not R based)so if you use the command ./fastqc /directoryOf_fastq/*.fastq it will run for all the fastq in that directory no mater you have 1 file or 100 file. And then after installing MultiQC just run multiqc command from the directory of fastqc.
I agree with Iva.
Both FastQC and MultiQC can be used also on Windows OS, using open platform https://usegalaxy.org. There you can find free NGS software for data analysis.
Best regards
Muliqc is used because it combines all the outputs from the fastq analysis, and it provides the one QC report for all of the processes samples. It is easy to compare on the report rather than numerous files. It summarizes the results of different bioinformatics tools in one sample. Whereas, fastqc proceed one sample at a time. Therefore, for each analysis, you have to generate multiple reports, and then compare all of the files separately. So, multiqc is a preferable option in quality control if you want to obtain the single report. Furthermore, after the fastqc of each sample, you need to run the multiqc again
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