Hi everyone,
I've recently released a new tool called MultiQC - it's a simple and quick command line tool that you point at a directory containing output from your analysis. It runs through all of the files and finds output that it recognises, building a single HTML report to summarise this information.
I wrote it because of the difficulty we have when generating hundreds of FastQC reports - it's impossible to go through all of these, so MultiQC makes one report with all of the samples plotted together in one place. This makes it very easy to spot any outliers and see trends.
This approach is generalised in MultiQC, with 12 other programs currently supported (see below). Output from any of these modules will be combined into a single report, meaning that you can follow the progress of each sample through your analysis pipeline.
You can find MultiQC here:
If you have Python & pip on your system, you can install MultiQC as follows:
See the documentation for more in depth instructions.
You can see a mini-poster that I made about the tool below. Any questions / requests / feedback welcome!
Phil
Currently supported tools:
I've recently released a new tool called MultiQC - it's a simple and quick command line tool that you point at a directory containing output from your analysis. It runs through all of the files and finds output that it recognises, building a single HTML report to summarise this information.
I wrote it because of the difficulty we have when generating hundreds of FastQC reports - it's impossible to go through all of these, so MultiQC makes one report with all of the samples plotted together in one place. This makes it very easy to spot any outliers and see trends.
This approach is generalised in MultiQC, with 12 other programs currently supported (see below). Output from any of these modules will be combined into a single report, meaning that you can follow the progress of each sample through your analysis pipeline.
You can find MultiQC here:
- http://multiqc.info/ - example reports and documentation
- Python Package Index (PyPI)
- GitHub - source code
If you have Python & pip on your system, you can install MultiQC as follows:
Code:
# install MultiQC pip install multiqc # run MultiQC multiqc <analysis_dir>
You can see a mini-poster that I made about the tool below. Any questions / requests / feedback welcome!
Phil
Currently supported tools:
- FastQC
- FastQ Screen
- Cutadapt
- Bismark
- STAR
- Tophat
- Bowtie
- Bowtie 2
- Subread featureCounts
- Picard MarkDuplicates
- Preseq
- Qualimap
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