I'm new to NGS anlysis, there are many QC (quality control ) software for NGS data, which one is best? I'm using https://usegalaxy.org so it's better to be available in this web sever. or is there any better program for QC to run on my laptop? is it heavy computation for a laptop (core i3 cpu and 4 Gb ram)?
I can recommend you MultiQC:
Ewels, Philip, et al. "MultiQC: summarize analysis results for multiple tools and samples in a single report." Bioinformatics 32.19 (2016): 3047-3048.
Fairly good integration of multiple tools, nice plots, etc.
It is within: "NGS: QC and manipulation" at https://usegalaxy.org, although I never used it there.
EDITED: now that I checked, it seems in galaxy you can only use multiqc for analyzing results. Well, in that case you can always use FastQC:
https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
It is a Java application that should not have very high computer resources requirements.
Finally, Illumina provides an official tool called Sequence Analysis Viewer:
https://support.illumina.com/sequencing/sequencing_software/sequencing_analysis_viewer_sav.html
Best regards.
I can recommend you MultiQC:
Ewels, Philip, et al. "MultiQC: summarize analysis results for multiple tools and samples in a single report." Bioinformatics 32.19 (2016): 3047-3048.
Fairly good integration of multiple tools, nice plots, etc.
It is within: "NGS: QC and manipulation" at https://usegalaxy.org, although I never used it there.
EDITED: now that I checked, it seems in galaxy you can only use multiqc for analyzing results. Well, in that case you can always use FastQC:
https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
It is a Java application that should not have very high computer resources requirements.
Finally, Illumina provides an official tool called Sequence Analysis Viewer:
https://support.illumina.com/sequencing/sequencing_software/sequencing_analysis_viewer_sav.html
Best regards.
There are many tools actually. If you find my book chapter useful, it could help you hopefully. Although title says it's basically about RNA-Seq data but you would get idea about many tools that apply to NGS data QC. Below is the link of my chapter.
https://link.springer.com/chapter/10.1007/978-94-024-1045-7_10
https://link.springer.com/chapter/10.1007/978-94-024-1045-7_10
I would suggest NGS QC toolkit which is very easy to use for quality check and filtering. For quality check only a very user friendly and visual software is fastaQC
FastQC is highly recommended for the quality check, the graphs generated are easy to understand specially for the beginners.
https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
fastaQC is so far one of the best for quick data quality check
I also like Qualimap because it will QC RNAseq data too.
http://qualimap.bioinfo.cipf.es/
Article NGS QC Toolkit: A Toolkit for Quality Control of Next Genera...
Please have a look. It has been given a list a of QC tool kits with comparison. I hope it would be helpful.
I have a problem downloading NGS QC Toolkit software. When I try to open the page I get an error message (like the page does not exist). I have written to the corresponding author a few days ago but no answer yet. Does anybody know how to get the software?
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