OMICtools is a workflow for genomic, transcriptomic, proteomic, and metabolomic data analysis. All tools have been classified by omic technologies (NGS, microarray, PCR, MS, NMR), applications and analytical steps. Publication: OMICtools: an informative directory for multi-omic data analysis

A5-miseq
  (5/5)
user-friendly, rapid and very useful!
Posted by Memol on Aug 26, 2015
TreeSeq
  (4/5)
I used readonly files as NGS-input and a small 16S FASTA database. Worked very fast.
Posted by Chris on Aug 12, 2015
CADD
  (5/5)
Combined Annotation Dependent Depletion (CADD) is a new tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome. Most of pathogenicity prediction algorithms tend to exploit a single information such as conservation to create a score. CADD give a broadly applicable metric that weights and integrated diverse information using a SVM approach. It integrates multiple annotations into one metric by contrasting variants that survived natural selection with simulated mutations.

Precomputed CADD scores can be downloaded on CADD website (http://cadd.gs.washington.edu/download). Scores have been included too in dbNSFP databases.

We have demonstrated that CADD is the most sensitive and specific prediction algorithms by comparison with the ClinVar, a database which aggregates information about genomic variation and its relationship to human health.
Posted by Pierre-Julien VIAILLY on Aug 03, 2015
ANNOVAR
  (5/5)
ANNOVAR is a very useful Perl package for the annotation of genetic variants detected using NGS. Users can annotate VCF files (or other compatible formats) throw 3 modules :
- Gene-based annotations : identify wether SNPs or CNVs cause protein coding changes using RefSeq, UCSC, ENSEMBL, GENCODE or AceView. Example : “Giving a list of variants in VCF format, what are the genes impacted ?”
- Region-based annotations : identify variants in a specific genomic region. Example : “Giving a list of differentially methylated regions, what are the genes in these loci ?”
- Filter-based annotations : identify variants that are reported in specific databases such as dbNSFP (pathogenicity prediction algorithms), dbSNP, 1000 genomes, ClinVar or COSMIC. Custom databases can be created in GFF format. Example : “Giving a list of variants, how can I find those previously reported as cancer-relevant mutations ?”

Giving a list of VCFs, ANNOVAR produces tab-separated values files which can be easily integrated in bioinformatics pipelines or directly read in a spreadsheet.
Posted by Pierre-Julien VIAILLY on Aug 03, 2015
Unipept
  (5/5)
Fast and accurate results and nice visualisations. Great tool!
Posted by Phil on Aug 01, 2015
edgeRun
I'm not able to download the EdgeRun package. I get the message that I need to buy the WinRaR.It looks like it is a spam. Please help me with downloading the EdgeRun program. I'm trying to normalize RNA seq data with the TMM method. My email address is sarah.abou-merhi@downstate.edu.

Thank you
Posted by Sara Irani on Aug 26, 2015
SNPper
Server is down again and the 502 Proxy Error is being shown.
Posted by CD on Aug 24, 2015
VENNY
May anybody tell me how to add a List of gene to the default 4 ones? i would need to compare 5 lists of gene and until now I could only compare 4.Thank you!
Posted by francesco on Aug 22, 2015
WhatsHap
No possible now access WhatsHap
Posted by Micky Estienne on Aug 21, 2015
CarrotDB
I can't access this database.
Posted by Silvia Bruznican on Aug 20, 2015