https://github.com/brentp/multiqc
Aggregate results from bioinformatics analyses across many samples into a single report.
Science Score: 23.0%
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Found 12 DOI reference(s) in README -
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Low similarity (11.6%) to scientific vocabulary
Last synced: 10 months ago
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Aggregate results from bioinformatics analyses across many samples into a single report.
Basic Info
- Host: GitHub
- Owner: brentp
- License: gpl-3.0
- Default Branch: master
- Homepage: http://multiqc.info
- Size: 20.6 MB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 1
- Open Issues: 0
- Releases: 0
Fork of MultiQC/MultiQC
Created over 6 years ago
· Last pushed over 6 years ago
https://github.com/brentp/MultiQC/blob/master/
#  ### Aggregate bioinformatics results across many samples into a single report. ##### Find [documentation](http://multiqc.info/docs) and [example reports](http://multiqc.info/examples/rna-seq/multiqc_report.html) at [http://multiqc.info](http://multiqc.info) [](https://pypi.python.org/pypi/multiqc/) [](https://anaconda.org/bioconda/multiqc) [](https://hub.docker.com/r/ewels/multiqc/) [](https://travis-ci.org/ewels/MultiQC) [](https://gitter.im/ewels/MultiQC) [](http://dx.doi.org/10.1093/bioinformatics/btw354) ----- MultiQC is a tool to create a single report with interactive plots for multiple bioinformatics analyses across many samples. MultiQC is written in Python (tested with v2.7, 3.4, 3.5 and 3.6). It is available on the [Python Package Index](https://pypi.python.org/pypi/multiqc/) and through conda using [Bioconda](http://bioconda.github.io/). Reports are generated by scanning given directories for recognised log files. These are parsed and a single HTML report is generated summarising the statistics for all logs found. MultiQC reports can describe multiple analysis steps and large numbers of samples within a single plot, and multiple analysis tools making it ideal for routine fast quality control. Currently, supported tools include: |Read QC & pre-processing | Aligners / quantifiers | Post-alignment processing | Post-alignment QC | |---------------------------------|-------------------------|-----------------------------|--------------------------------------| |[Adapter Removal][adapterremoval]|[BBMap][bbmap] |[Bamtools][bamtools] |[biobambam2][biobambam2] | |[AfterQC][afterqc] |[BISCUIT][biscuit] |[Bcftools][bcftools] |[BUSCO][busco] | |[Bcl2fastq][bcl2fastq] |[Bismark][bismark] |[GATK][gatk] |[Conpair][conpair] | |[BBTools][bbmap] |[Bowtie][bowtie-1] |[HOMER][homer] |[DamageProfiler][damageprofiler] | |[BioBloom Tools][biobloomtools] |[Bowtie 2][bowtie-2] |[HTSeq][htseq] |[DeDup][dedup] | |[ClipAndMerge][clipandmerge] |[HiCUP][hicup] |[MACS2][macs2] |[deepTools][deeptools] | |[Cluster Flow][clusterflow] |[HiC-Pro][hicpro] |[Picard][picard] |[Disambiguate][disambiguate] | |[Cutadapt][cutadapt] |[HISAT2][hisat2] |[Prokka][prokka] |[goleft][goleft] | |[leeHom][leehom] |[Kallisto][kallisto] |[RSEM][rsem] |[HiCExplorer][hicexplorer] | |[InterOp][interop] |[Long Ranger][longranger]|[Samblaster][samblaster] |[methylQA][methylqa] | |[FastQC][fastqc] |[Salmon][salmon] |[Samtools][samtools] |[miRTrace][mirtrace] | |[FastQ Screen][fastq-screen] |[Slamdunk][slamdunk] |[SnpEff][snpeff] |[mosdepth][mosdepth] | |[Fastp][fastp] |[STAR][star] |[Subread featureCounts][featurecounts]|[Peddy][peddy] | |[FLASh][flash] |[Tophat][tophat] |[Stacks][stacks] |[phantompeakqualtools][phantompeakqualtools]| |[Flexbar][flexbar] | |[THetA2][theta2] |[Preseq][preseq] | |[Jellyfish][jellyfish] | | |[QoRTs][qorts] | |[KAT][kat] | | |[Qualimap][qualimap] | |[MinIONQC][minionqc] | | |[QUAST][quast] | |[Skewer][skewer] | | |[RNA-SeQC][rna_seqc] | |[SortMeRNA][sortmerna] | | |[RSeQC][rseqc] | | | | |[Sargasso][sargasso] | | | | |[Supernova][supernova] | | | | |[VCFTools][vcftools] | | | | |[VerifyBAMID][verifybamid] | MultiQC can also easily parse data from custom scripts, if correctly formatted / configured. See the [MultiQC documentation](http://multiqc.info/docs/#custom-content) for more information. Please note that some modules only recognise output from certain tool subcommands. Please follow the links in the above table to the [module documentation](http://multiqc.info/docs/#multiqc-modules) for more information. More modules are being written all of the time. Please suggest any ideas as a new [issue](https://github.com/ewels/MultiQC/issues) _(include an example log file if possible)_. ## Installation You can install MultiQC from [PyPI](https://pypi.python.org/pypi/multiqc/) using `pip` as follows: ```bash pip install multiqc ``` Alternatively, you can install using [Conda](http://anaconda.org/) from the [bioconda channel](https://bioconda.github.io/): ```bash conda install -c bioconda multiqc ``` If you would like the development version instead, the command is: ```bash pip install --upgrade --force-reinstall git+https://github.com/ewels/MultiQC.git ``` MultiQC is also available in the [Galaxy Toolshed](https://toolshed.g2.bx.psu.edu/view/engineson/multiqc/). ## Usage Once installed, you can use MultiQC by navigating to your analysis directory (or a parent directory) and running the tool: ```bash multiqc . ``` That's it! MultiQC will scan the specified directory (`.` is the current dir) and produce a report detailing whatever it finds. The report is created in `multiqc_report.html` by default. Tab-delimited data files are also created in `multiqc_data/`, containing extra information. These can be easily inspected using Excel (use `--data-format` to get `yaml` or `json` instead). For more detailed instructions, run `multiqc -h` or see the [documentation](http://multiqc.info/docs/#running-multiqc). ## Citation Please consider citing MultiQC if you use it in your analysis. > **MultiQC: Summarize analysis results for multiple tools and samples in a single report**
> _Philip Ewels, Mns Magnusson, Sverker Lundin and Max Kller_
> Bioinformatics (2016)
> doi: [10.1093/bioinformatics/btw354](http://dx.doi.org/10.1093/bioinformatics/btw354)
> PMID: [27312411](http://www.ncbi.nlm.nih.gov/pubmed/27312411) ```TeX @article{doi:10.1093/bioinformatics/btw354, author = {Ewels, Philip and Magnusson, Mns and Lundin, Sverker and Kller, Max}, title = {MultiQC: summarize analysis results for multiple tools and samples in a single report}, journal = {Bioinformatics}, volume = {32}, number = {19}, pages = {3047}, year = {2016}, doi = {10.1093/bioinformatics/btw354}, URL = { + http://dx.doi.org/10.1093/bioinformatics/btw354}, eprint = {/oup/backfile/Content_public/Journal/bioinformatics/32/19/10.1093_bioinformatics_btw354/3/btw354.pdf} } ``` ## Contributions & Support Contributions and suggestions for new features are welcome, as are bug reports! Please create a new [issue](https://github.com/ewels/MultiQC/issues) for any of these, including example reports where possible. MultiQC has extensive [documentation](http://multiqc.info/docs) describing how to write new modules, plugins and templates. There is a chat room for the package hosted on Gitter where you can discuss things with the package author and other developers: https://gitter.im/ewels/MultiQC If in doubt, feel free to get in touch with the author directly: [@ewels](https://github.com/ewels) (phil.ewels@scilifelab.se) ### Contributors Project lead and main author: [@ewels](https://github.com/ewels) Code contributions from: [@ahvigil](https://github.com/ahvigil), [@aledj2](https://github.com/aledj2), [@apeltzer](https://github.com/apeltzer), [@avilella](https://github.com/avilella), [@boulund](https://github.com/boulund), [@bschiffthaler](https://github.com/bschiffthaler), [@chuan-wang](https://github.com/chuan-wang), [@cpavanrun](https://github.com/cpavanrun), [@dakl](https://github.com/dakl), [@ehsueh](https://github.com/ehsueh), [@epruesse](https://github.com/epruesse), [@florianduclot](https://github.com/florianduclot/), [@guillermo-carrasco](https://github.com/guillermo-carrasco), [@HLWiencko](https://github.com/HLWiencko), [@iimog](https://github.com/iimog), [@joachimwolff](https://github.com/joachimwolff), [@jrderuiter](https://github.com/jrderuiter), [@lpantano](https://github.com/lpantano), [@matthdsm](https://github.com/matthdsm), [@MaxUlysse](https://github.com/MaxUlysse), [@mlusignan](https://github.com/mlusignan), [@moonso](https://github.com/moonso), [@noirot](https://github.com/noirot), [@remiolsen](https://github.com/remiolsen), [@rdali](https://github.com/rdali), [@rlegendre](https://github.com/rlegendre), [@robinandeer](https://github.com/robinandeer), [@Rotholandus](https://github.com/Rotholandus), [@sachalau](https://github.com/sachalau/), [@t-neumann](https://github.com/t-neumann), [@vladsaveliev](https://github.com/vladsaveliev), [@winni2k](https://github.com/winni2k), [@wkretzsch](https://github.com/wkretzsch), [@nservant](https://github.com/nservant), and many others. Thanks for your support! MultiQC is released under the GPL v3 or later licence. [adapterremoval]: http://multiqc.info/docs/#adapter-removal [afterqc]: http://multiqc.info/docs/#afterqc [bamtools]: http://multiqc.info/docs/#bamtools [bbmap]: http://multiqc.info/docs/#bbmap [bcftools]: http://multiqc.info/docs/#bcftools [bcl2fastq]: http://multiqc.info/docs/#bcl2fastq [biobambam2]: http://multiqc.info/docs/#biobambam2 [biobloomtools]: http://multiqc.info/docs/#biobloom-tools [biscuit]: http://multiqc.info/docs/#biscuit [bismark]: http://multiqc.info/docs/#bismark [bowtie-1]: http://multiqc.info/docs/#bowtie-1 [bowtie-2]: http://multiqc.info/docs/#bowtie-2 [busco]: http://multiqc.info/docs/#busco [clipandmerge]: http://multiqc.info/docs/#clipandmerge [clusterflow]: http://multiqc.info/docs/#cluster-flow [conpair]: http://multiqc.info/docs/#conpair [cutadapt]: http://multiqc.info/docs/#cutadapt [damageprofiler]: http://multiqc.info/docs/#damageprofiler [dedup]: http://multiqc.info/docs/#dedup [deeptools]: http://multiqc.info/docs/#deeptools [disambiguate]: http://multiqc.info/docs/#disambiguate [fastq-screen]: http://multiqc.info/docs/#fastq-screen [fastqc]: http://multiqc.info/docs/#fastqc [fastp]: http://multiqc.info/docs/#fastp [featurecounts]: http://multiqc.info/docs/#featurecounts [flash]: http://multiqc.info/docs/#flash [flexbar]: http://multiqc.info/docs/#flexbar [gatk]: http://multiqc.info/docs/#gatk [goleft]: http://multiqc.info/docs/#goleft-indexcov [hicexplorer]: http://multiqc.info/docs/#hicexplorer [hicup]: http://multiqc.info/docs/#hicup [hicpro]: http://multiqc.info/docs/#hic-pro [hisat2]: http://multiqc.info/docs/#hisat2 [homer]: http://multiqc.info/docs/#homer [htseq]: http://multiqc.info/docs/#htseq [interop]: http://multiqc.info/docs/#interop [jellyfish]: http://multiqc.info/docs/#jellyfish [kallisto]: http://multiqc.info/docs/#kallisto [kat]: http://multiqc.info/docs/#kat [leehom]: http://multiqc.info/docs/#leehom [longranger]: http://multiqc.info/docs/#longranger [macs2]: http://multiqc.info/docs/#macs2 [methylqa]: http://multiqc.info/docs/#methylqa [minionqc]: http://multiqc.info/docs/#minionqc [mirtrace]: http://multiqc.info/docs/#mirtrace [mosdepth]: http://multiqc.info/docs/#mosdepth [peddy]: http://multiqc.info/docs/#peddy [phantompeakqualtools]: http://multiqc.info/docs/#phantompeakqualtools [picard]: http://multiqc.info/docs/#picard [preseq]: http://multiqc.info/docs/#preseq [prokka]: http://multiqc.info/docs/#prokka [qorts]: http://multiqc.info/docs/#qorts [qualimap]: http://multiqc.info/docs/#qualimap [quast]: http://multiqc.info/docs/#quast [rna_seqc]: http://multiqc.info/docs/#rna_seqc [rsem]: http://multiqc.info/docs/#rsem [rseqc]: http://multiqc.info/docs/#rseqc [salmon]: http://multiqc.info/docs/#salmon [samblaster]: http://multiqc.info/docs/#samblaster [samtools]: http://multiqc.info/docs/#samtools [sargasso]: http://multiqc.info/docs/#sargasso [skewer]: http://multiqc.info/docs/#skewer [slamdunk]: http://multiqc.info/docs/#slamdunk [snpeff]: http://multiqc.info/docs/#snpeff [sortmerna]: http://multiqc.info/docs/#sortmerna [stacks]: http://multiqc.info/docs/#stacks [star]: http://multiqc.info/docs/#star [supernova]: http://multiqc.info/docs/#supernova [theta2]: http://multiqc.info/docs/#theta2 [tophat]: http://multiqc.info/docs/#tophat [trimmomatic]: http://multiqc.info/docs/#trimmomatic [vcftools]: http://multiqc.info/docs/#vcftools [verifyBAMID]: http://multiqc.info/docs/#verifybamid
Owner
- Name: Brent Pedersen
- Login: brentp
- Kind: user
- Location: Oregon, USA
- Twitter: brent_p
- Repositories: 220
- Profile: https://github.com/brentp
Doing genomics