OMICtools can help a) experimental researchers/clinicians find appropriate tools for their needs b) developers to stay up to date and to avoid redundancy c) funding agencies to ensure that the submitted projects are high value-added. Do you want help us to improve OMICtools? Call for curators

(Henry et al., 2014) OMICtools: an informative directory for multi-omic data analysis. Database.

ProteoWizard
  (4/5)
Proteowizard written in C ++, provides a clear and readable interface programming. It is based on modern design and application of new standards c ++ 11 (including smart pointers). It also provides many algorithms for processing data spectrometry (peak picking ...) and allows the reading of many raw files owners. This is an indispensable tool for application developers proteomics / metabolomics. The only downside is that it still uses a build system based on bjam that requires a long learning curve.
Posted by Marc Dubois on Oct 21, 2014
BiGG
  (5/5)
A must in genome scale metabolic networks.
Posted by Marouen Ben Guebila on Oct 20, 2014
SSAKE
  (5/5)
Ssake is super easy to use and produces accurate results.
It is lightweight and has no dependencies, I highly recommend it. Because it uses coverage info, assemblies are stratified which makes it also suitable for transcriptome and meta genome assemblies. It is not as greedy as most people report, the correct path is chosen no based on longest overlap, but coverage and reads having a matching pairing partner already assembled
Posted by Nick on Oct 18, 2014
CHANCE
  (2/5)
Not ideal to me because as far as I know, it's impossible to use it with command line... I had difficulties to open .bam files...
Posted by Fabien Pichon on Oct 17, 2014
phantompeakqualtools
  (5/5)
Indispensable for ChIP-seq and ATAC-seq quality control. Produces a graph showing the crosscorrelation of reads distributions on forward and reverse strand as well as ratios to estimate the noise. Be carefull however, because these ratios are meaningfull only for narrow peaks, not for broad peaks like H3K27me3 or H3K36me3.
Posted by Fabien Pichon on Oct 17, 2014
F-Seq
  (4/5)
Used for FAIRE-seq. Usefull for noisy data, but a little bit complex to use, but still less complex than ZINBA. You have to generate background .bff files with the help of GEM tools and convert .mappability file into .wig file, but .iff files are more obscure. Fortunately, Furey's lab provided some generic ones. Nonetheless I never could reproduce exactly their peak calling using ENCODE data... it seems there is a part of randomness in the process. Also, note that you need an additionnal perl script to calculate peaks p-values !
Posted by Fabien Pichon on Oct 17, 2014
PFMS
  (4/5)
Usefull if you want to run several peak callers on the same samples without loosing your time ! You can then only use consensus peaks to win specificity, but is it really necessary to run several peaks callers on all experiments ? Depends on your data and how noisy they are.
Posted by Fabien Pichon on Oct 17, 2014
BreakDancer
Hi there,
when I run "make" during the installation process I receive the following output:

[ 14%] Built target boost-libs
[ 15%] Performing build step for 'samtools-lib'
make[2]: *** [vendor/src/samtools-lib-stamp/samtools-lib-build] Errore 2
make[1]: *** [CMakeFiles/samtools-lib.dir/all] Errore 2
make: *** [all] Errore 2
salvo@linux-t9bq:~/breakdancer/build> su -x "make clean"
su: opzione non valida -- "x"
Try 'su --help' for more information.
salvo@linux-t9bq:~/breakdancer/build> su -c "make clean"
Password:
salvo@linux-t9bq:~/breakdancer/build> su -c "make"
Password:
[ 1%] Creating directories for 'boost-libs'
[ 3%] Performing download step (verify and extract) for 'boost-libs'
-- verifying file...
file='/home/salvo/breakdancer/vendor/boost-1.54-breakdancer.tar.gz'
-- verifying file... warning: did not verify file - no URL_MD5 checksum argument? corrupt file?
-- extracting...
src='/home/salvo/breakdancer/vendor/boost-1.54-breakdancer.tar.gz'
dst='/home/salvo/breakdancer/build/vendor/boost/boost-src'
-- extracting... [tar xfz]
-- extracting... [analysis]
-- extracting... [rename]
-- extracting... [clean up]
-- extracting... done
[ 5%] No patch step for 'boost-libs'
[ 7%] No update step for 'boost-libs'
[ 8%] Performing configure step for 'boost-libs'
Building Boost.Build engine with toolset gcc... tools/build/v2/engine/bin.linuxx86_64/b2
Detecting Python version... 2.7
Detecting Python root... /usr
Unicode/ICU support for Boost.Regex?... not found.
Generating Boost.Build configuration in project-config.jam...

Bootstrapping is done. To build, run:

./b2

To adjust configuration, edit 'project-config.jam'.
Further information:

- Command line help:
./b2 --help

- Getting started guide:
http://www.boost.org/more/getting_started/unix-variants.html

- Boost.Build documentation:
http://www.boost.org/boost-build2/doc/html/index.html

[ 10%] Performing build step for 'boost-libs'
[ 12%] No install step for 'boost-libs'
[ 14%] Completed 'boost-libs'
[ 14%] Built target boost-libs
[ 15%] Creating directories for 'samtools-lib'
[ 17%] Performing download step (verify and extract) for 'samtools-lib'
-- verifying file...
file='/home/salvo/breakdancer/vendor/samtools-0.1.19.tar.gz'
-- verifying file... warning: did not verify file - no URL_MD5 checksum argument? corrupt file?
-- extracting...
src='/home/salvo/breakdancer/vendor/samtools-0.1.19.tar.gz'
dst='/home/salvo/breakdancer/build/vendor/samtools'
-- extracting... [tar xfz]
-- extracting... [analysis]
-- extracting... [rename]
-- extracting... [clean up]
-- extracting... done
[ 19%] No patch step for 'samtools-lib'
[ 21%] No update step for 'samtools-lib'
[ 22%] Performing configure step for 'samtools-lib'
Building samtools, build log at /home/salvo/breakdancer/build/vendor/samtools/build.log
[ 24%] Performing build step for 'samtools-lib'
make[2]: *** [vendor/src/samtools-lib-stamp/samtools-lib-build] Errore 2
make[1]: *** [CMakeFiles/samtools-lib.dir/all] Errore 2
make: *** [all] Errore 2

Salvo
email: salvatore_camiolo@yahoo.it
Posted by Salvo on Oct 21, 2014
F-Seq
F-Seq tool has been moved into "Peak detection". Thank you.
Posted by Arnaud Desfeux on Oct 17, 2014
F-Seq
This is a peak caller, not for motif discovery ! Should be moved !
Posted by fabien pichon on Oct 17, 2014
COV2HTML
Dear Marc,

I have moved COV2HTML into "Data visualization".

Best regards,
Arnaud
Posted by Arnaud Desfeux on Oct 17, 2014
COV2HTML
Could you move COV2HTML into "Data visualization",
Best Regards,
Marc
--
Dr Marc Monot - PhD - Institut Pasteur
Laboratoire Pathogenese des Bacteries Anaerobies
25 rue du docteur roux 75015 Paris
Phone / Fax. +33145688390 ; +33140613123
Webpage. http://www.mmonot.eu
Posted by Monot on Oct 16, 2014
RCGDB
The Roche Cancer Genome Database cannot be accessed.
Posted by Euphemia on Oct 15, 2014
SNPper
the site is not working … please fix it
Posted by iconforbest on Oct 15, 2014