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.

fastcore
  (5/5)
FASTCORE is available here
http://wwwen.uni.lu/recherche/fstc/life_sciences_research_unit/research_areas/systems_biology/software
Posted by Maria Pires Pacheco on Oct 30, 2014
VENNY
  (5/5)
Very useful tool to obtain a Venn diagram from up to 4 lists
Posted by Sonia on Oct 28, 2014
BEDTools
  (5/5)
Another indispensable tools suite to have, particularly if you work with .bed files, of course !
In comparison, however, Homer is better if you want to intersect further files because it gives more details, ideal to create a Venn diagram !
A big plus of bedtools : tools are very well documented, with schemes ! I like: "shuffle" to randomly relocate peaks, to test significance of a pathway enrichment for example !
Posted by fabien pichon on Oct 27, 2014
RSEM
  (5/5)
Usefull if you want to estimate isoform expression in your RNA-seq. It uses Bowtie by default but you can map with another mapper and just use BAM/SAM file, so RSEM is quite flexible. Routinely used in TCGA workflow, but I would like to highlight that their RSEM UCSC isoforms IDs are sometimes different from Official UCSC isoforms IDs, no idea why...
Posted by Fabien Pichon on Oct 27, 2014
Bowtie
  (5/5)
One of the most commonly used mapper. Very efficient and fast. Be carefull however with paired-end reads because Bowtie do not take into account pairs where only one read is properly mapped. I would thus prefer Bowtie2 for paired-end reads. Of note in Bowtie2 : -m option has disappeared... what a pity !
Posted by Fabien Pichon on Oct 27, 2014
ASCAT
  (5/5)
For CNV identification. Works well. The paper is very clear, very well explained ! A lot of usefull plots. Sometimes, it cannot resolve the couple (ploidy, aberrent fraction cell) shown in the sunrise plot. I thus used Noise-free-CNV-filter to normalize data before ASCAT, but it didn't help to resolve these samples. Hopefully, Peter van Loo has added the possibility to manually define it in the new version.
Posted by Fabien Pichon on Oct 27, 2014
CEAS
  (3/5)
I used it for ChIP-seq, to annotate Peaks. But I also used Homer tools and results were quite different.... for example in 5'-UTR (4.1% vs 2.4%). I guess it comes from the definition of what a region is, but I used a small file of 10 peaks and CEAS returned strange percentages... I think that CEAS splits a peak if it can fit in 2 regions, to check... I like the pie charts representation.
Posted by Fabien Pichon on Oct 27, 2014
Gemi
According to the developers: "Gemi accepts aligned sequences in fasta format. It is default to be obtained from any alignment tool. Within the package, another software to transfer aln to fasta format.
By default, Gemi checks if the sequences are aligned or not. If not, an error message appears."
Posted by Vincent J Henry on Oct 30, 2014
Gemi
Will not load any files, they are in fasta format?
Posted by K on Oct 29, 2014
OptiType
This is a software on HLA typing, which deals mostly with variant calling/phasing. While related to immunology and highly critical to immunity studies, it is technically different from RepSeq which deals with metagenome-like that contains a diverse set of highly dissimilar sequences. Please consider moving to Variant calling section/etc
Posted by Mikhail Shugay on Oct 29, 2014
ngs.plot
This not a Genome browser. This a "Plot maker"... Difficult to place it, indeed... It creates heatmaps that I commonly use for Quality Control.
Posted by Fabien Pichon on Oct 27, 2014
Platanus
The source code is still not availabe, although they said they will make it public "ASAP" couple months ago
Posted by Kevin on Oct 24, 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