Comments on Software for Genomics

[Richard Finney]

I have a list of software that our organization deploys. I usually concentrate on open source tools to analyze genomics data with notable execptions of novoalign and Excel.
I am looking for user comments on how good some commercial/third party software solutions are.

The list is ...

Software Name Manufacturer
Analytica Lumina Decision Systems
BIOBASE BIOBASE (Qiagen)
ChemBioOffice Ultra 2008 CambridgeSoft Corp. (Perkin Elmer)
CLC Genomics Workbench Qiagen (CLC bio)
EndNote Thomson Reuters (Scientific)
FlowJo Cytometry Tree Star Inc.
Geneious Pro Biomatters, Inc.
GenePix Pro 6 MDS Analytical Technologies
GeneSpring Agilent Technologies Inc.
Genomatix Suite Genomatix Software
Genome Analyzer - Genomatix Mining Station (GMS) and Genomatix Genome Analyer (GGA) Genomatix Software
GraphPad Prism GraphPad Software, Inc.
High Performance Computing/Data Management
ImageQuant TL GE Healthcare Bio-Sciences Corp
Ingenuity Pathways Analysis (IPA)QIAGEN Redwood City
iReview/JReview Integrated Clinical Systems, Inc.
JMP SAS Institute Inc.
KaleidaGraph Synergy Software
Labmatrix BioFortis, Inc.
Lasergene DNASTAR, Inc.
MacVector MacVector, Inc.
Mathematica Wolfram Research, Inc.
MetaCore Thomson Reuters
Nexus Copy Number BioDiscovery, Inc.
Partek Genomics Suite Partek Inc.
Pathway Studio Enterprise Ariadne Genomics Inc.
Quosa Elsevier
Reference Manager (user's info)
SAS SAS Institute Inc.
ScienceSlides VisiScience Corp.
Sequencher Gene Codes Corporation
SigmaPlot Systat Software, Inc.
SPSS IBM Corporation
Stat/Transfer Circle Systems, Inc.
Stata/SE StataCorp LP
StatXact Cytel Inc.
SUDAAN Research Triangle Institute
TIBCO Spotfire S+ TIBCO Software Inc,
Vector NTI Suite Invitrogen (Life Technologies)

Rather that just list features, I'd like to get your opinions.
So any commentary, thumbs up, thumbs down, etc. on the usefulness on any of these (or others that you can think of) would be appreciated.

[GenoMax]

Folks please don't start a discussion (war) about commercial versus open source software.

@Richard's question is specifically about what people find useful/bad about the list of software posted so answers should stay focused on that aspect.

[GenoMax]

Since most of these packages cost a pretty penny they must still be providing some useful benefit for a section of users in your workplace. Hopefully someone monitors usage and decides what gets renewed (since most probably have/need a maintenance contract to receive updates). People often make the error of assuming that if you don't personally like/use a software then no one else likes/needs it either.

Vector NTI is the grand daddy of bioinformatics software and it has been around for so long that many labs have year's worth of data stored in their local VNTI databases. It is a miracle but the original Vector NTI suite still works all the way on Windows 10 (there are parts in there that are probably from mid-90s, Jet database engine). Vector NTI Express for PC/Mac is a total java rewrite (so a completely separate program suite) that is more current (and has most of the functionality of original Vector NTI Suite) and is more frequently updated. Vector NTI is like old slippers, for many. People are used to it and its interface.

DNASTAR is pretty popular with folks who do Sanger sequencing. Its feature set for handling Sanger data overlaps largely with Sequencher. Different bits of DNASTAR require a different level of purchase.

Ingenuity Pathway Analysis can save someone tons of time if you work in human/mouse/rat systems since their integrated knowledgebase is human curated and can create a story from a list of genes (provided you have a sane result to begin with) with a few clicks.

SAS/SPSS is kind of like Vector NTI. If you learned SAS/SPSS a long time ago and have used it since then nothing is going to tempt these people to go to R or anything else.

CLC Genomics Workbench is perhaps the most comprehensive single package that wraps many core NGS data analysis methodologies in one relatively easy to use Java program. Additional functionality is enabled by "plug-in's" which sometimes require their own separate licenses. If one is analyzing a simple straight forward dataset then CLC requires the least amount of activation energy to get started with NGS data analysis.

[cmccabe]

I have been using nexus copy number for many years (primarily for array cgh. It it very easy to use, flexible (both platfom independent and runs in windows, mac, and linux), and newest version of (nxclinical) will have additional ngs capabilities. I hope this helps .

[dariober]

My 2p:

EndNote: Myself and others around me have switched to Mendeley and we are quite happy with it. I haven't been too impressed by Endnote and sometimes I got troubles making it work, possibly because I wasn't using it properly. In any case, Mendeley is free and for what I need is at least as good, if not better, so the choice is obvious to me.

[prathimads]

Would like to add Strand NGS software to the above list.
Strand NGS is an integrated platform that provides analysis, management and visualization tools for next generation sequencing (NGS) data with desktop/ server versions and includes a feature-rich Genome Browser that provides custom visualizations to support the interpretation of analysis results.
Supports alignment and analysis of RNA-Seq, DNA-Seq, small RNA, Methyl-Seq, MeDIP-Seq and ChIP-Seq data, as well as biological interpretation, including Pathway and Multi-omic analysis. (http://www.strand-ngs.com/)

[Macspider]

For what concerns me, I didn't use many of these but for the ones I used, Thumbs up for Geneious Pro and Mathematica.