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toggle navigation current version: v1.5 home docs plugins logo example reports analysis types rna-seq whole genome bisulfite hi-c customisation _ngi plugin aggregate results from bioinformatics analyses across many samples into a single report searches a given directory for analysis logs and compiles a html report. it's a general use tool, perfect for summarising the output from numerous bioinformatics tools. video introduction to (1:19) video installing (4:33) video running (5:21) video using reports (6:06) github python package index documentation 61 supported tools publication / citation get help on gitter example report quick install pip install # install . # run conda install -c bioconda . git clone https://github.com/ewels/.git python setup.py install . pip conda manual need a little more help? see the full installation instructions . example reports rna-seq whole-genome sequencing methylation (bisfulite) genome structure (hi-c) customised with _ngi plugin this report was generated using logs from an analysis accidentally run on chip-seq data from the bi human reference epigenome mapping project: chip-seq in human subject dataset ( srp001534 ). initial qc was done using fastqc , followed by trimming with trimgalore! (a wrapper around cutadapt ). reads were aligned using star and overlaps counted with featurecounts . rseqc package was used to check various quality control aspects of the data. -- download report download logs you can download this report and / or the logs used to generate it, to try running yourself. the data from this report comes from an analysis of hapmap trio samples, run by the national genomics infrastructre (ngi) at scilifelab, sweden. initial quality control was done using fastqc and fastq screen . reads were processed with gatk and the aligned reads analysed using picard . downstream qc was done using qualimap bamqc and snpeff . download report download logs you can download this report and / or the logs used to generate it, to try running yourself. note that the example report has some user-specific config settings, seen in the _config.yaml file. the example methylation report is based on analysis of data from the geo ncbi project gse47966 , from the 2013 lister et. al. paper global epigenomic reconfiguration during mammalian brain development . raw data was run through fastqc and trimmed using trim galore! (a wrapper around cutadapt ). reads were aligned, deduplicated and cytosine methylation statuses called using bismark . download report download logs you can download this report and / or the logs used to generate it, to try running yourself. this hi-c report was generated using hi-c data from louise harewood at cruk cambridge institute . reads were run through fastqc and then processed using hicup (hi-c user pipeline). download report download logs you can download this report and / or the logs used to generate it, to try running yourself. note that the example report has some user-specific config settings, seen in the _config.yaml file. this report was generated in combination with the _ngi plugin. this plugin adds a few new functionalities to which are specific to the scilifelab national genomics infrastruture . a new report template ( ngi ) styles reports with our logo. a new module ( ngi-rnaseq ) adds sample similarity plots generated from custom code in our rna pipeline . it also loads intersting data fields from our lims (eg. rin score) and puts these into the report. finally, it saves the parsed biofinformatics summary results back in the lims for multi-project meta analyses. download report download logs you can download this report and / or the logs used to generate it, to try running yourself. the _ngi package must be installed. note that the example report has some user-specific config settings, seen in the _config.yaml file. it can also be run with the --test-db parameter, using the example data provided . example reports _ngi hi-c bisulfite seq whole-genome seq rna-seq ever spent ages collecting reports and wading through log file output? here's the answer to your frustrations... visualise statistics from your pipeline collects numerical stats from each module at the top the report, so that you can track how your data behaves as it proceeds through your analysis. view example report plot all of your samples together visualizing your samples together allows detailed comparison, not possible by scanning one report after another. example reports analysis types rna-seq whole genome bisulfite hi-c supports your favourite tools comes supports many common bioinformatics tools out of the box. if you're missing something, just create an issue on github to request it - if you have an example log file it's usually pretty fast. view available modules adapter removal afterqc bcl2fastq biobloom tools cluster flow cutadapt clipandmerge fastq screen fastqc flexbar interop jellyfish leehom skewer sortmerna trimmomatic bismark bowtie 1 bowtie 2 bbmap hicup hisat2 kallisto longranger salmon star tophat bamtools bcftools busco conpair disambiguate dedup deeptools featurecounts gatk goleft indexcov hicexplorer homer htseq macs2 methylqa peddy picard preseq prokka qorts qualimap quast rna-seqc rsem rseqc samblaster samtools sargasso slamdunk snpeff supernova theta2 vcftools verifybamid extensible and documented want to use this to do something fancy? is structured to allow easy extension and customisation with plugin hooks, a submodule framework and simple templating. everything is well documented, with step by step instructions for writing your new tool. read the docs nice things that people have said about amazingly, https://t.co/qtdfcmvg3b just works. ran ` .` in a dir with bunch of star, featurecounts, fastqc results. worked 1st time. — stephen turner (@genetics_blog) may 31, 2016 @tallphil after using for 1 month, already uncovered discrepancy across samples on a project — mike love (@mikelove) 17 june 2016 == awesome tool! wish all bioinfo software were as documented, modular and useful as this! https://t.co/oidazlnqxs — andré rendeiro (@afrendeiro) february 26, 2016 comment from discussion now published! tool for summarising & visualising bioinfo results. . @tallphil this such a great difference to the visualization of fastqc reports individually! :) — olalla lorenzo (@o_olalla) june 21, 2016 really impressed by this tool - create automatic bioinfo reports: usage: https://t.co/edumwoxyn1 reports: https://t.co/psrsuh5egi — eric normandeau (@eric_normandeau) may 25, 2016 can recommend : creates pretty report of -all- output from fastqc,bowtie,samtools,etc https://t.co/cxbv6nxmq8 pic.twitter.com/4ha4aupoki — elin videvall (@elinvidevall) april 6, 2016 @tallphil just blew my mind. great stuff. — stephen newhouse (@s_j_newhouse) july 18, 2016 @elinvidevall @biomickwatson @tallphil this is a fantastic tool i use frequently for single cell qc. glad to see it published. — sowmya iyer (@becausebiology) 17 june 2016 current favourite tool - - https://t.co/vsaas128gj - piece of cake to use, essential for large projects, thanks very much @tallphil — lavinia gordon (@mrslaviniag) 2 july 2016 i'm continuously impressed by how slick from @tallphil is. it makes my life so much easier. — devon ryan (@dpryan79) 30 august 2016 fantastic tool! combine 100s of fastqc files and alignment scores into a single report within minutes... https://t.co/2q0axkwel3 — jana sperschneider (@jsperschneider) september 7, 2016 see more on twitter.com → live discussion about on gitter.im -- simple installation search any directory view report in a web browser zip file for easy sharing extensible & well documented install from the python package index or bioconda to install , simply run pip install on the command line. if you use conda, you can run conda install -c bioconda instead. see the installation instructions for more help. documentation view on github view on pypi created by phil ewels: ewels | tallphil | linkedin | researchgate × : suppo

URL analysis for multiqc.info

http://www.multiqc.info//examples/ngi-rna/ngi_db_data.json
http://www.multiqc.info//docs/#rna-seqc
http://www.multiqc.info//docs/#fastqc
http://www.multiqc.info//docs/#skewer
http://www.multiqc.info//docs/#bismark
http://www.multiqc.info//docs/#bamtools
http://www.multiqc.info//docs/#bcl2fastq
http://www.multiqc.info//examples/hi-c/multiqc_config.yaml
http://www.multiqc.info//docs/#hisat2
http://www.multiqc.info//examples/ngi-rna/test_ngi_project_multiqc_report.html
http://www.multiqc.info//docs/#jellyfish
http://www.multiqc.info//docs/#cutadapt
http://www.multiqc.info//examples/wgs/multiqc_report.zip
http://www.multiqc.info//docs/#fastq-screen
http://www.multiqc.info//docs/#trimmomatic
cambridgecancer.org.uk
bioinformatics.babraham.ac.uk

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  NAME Philip Ewels

ADDRESS

STREET
Science for Life Laboratory
Box 1031

  CITY Solna

  STATE Stockholm

  PCODE 17121

  COUNTRY SE

  PHONE +46.852481435

  EMAIL [email protected]

ADMIN

  HANDLE C163116977-LRMS

  NAME Philip Ewels

ADDRESS

STREET
Science for Life Laboratory
Box 1031

  CITY Solna

  STATE Stockholm

  PCODE 17121

  COUNTRY SE

  PHONE +46.852481435

  EMAIL [email protected]

TECH

  HANDLE C163116976-LRMS

  NAME Philip Ewels

ADDRESS

STREET
Science for Life Laboratory
Box 1031

  CITY Solna

  STATE Stockholm

  PCODE 17121

  COUNTRY SE

  PHONE +46.852481435

  EMAIL [email protected]

BILLING

  HANDLE C163116978-LRMS

  NAME Philip Ewels

ADDRESS

STREET
Science for Life Laboratory
Box 1031

  CITY Solna

  STATE Stockholm

  PCODE 17121

  COUNTRY SE

  PHONE +46.852481435

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