Jitendra Narayan
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List of popular bioinformatics software/tools
By Jitendra Narayan 4146 days ago Comments (28)
http://samtools.sourceforge.net/swlist.shtml
In current genome era, our day to day work is to handle the huge geneome sequences, expression data, several other datasets. This link provide a comprehensive list of commonly used sofware/tools.
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This wikipedia page also list good, and useful software for bioinformatics analysis work.
Link @ http://en.wikipedia.org/wiki/List_of_open-source_bioinformatics_software
The University of Michigan's bioinformatics software links is pretty impressive. It provide short description of each software/tool as well.
Link @ http://www.ccmb.med.umich.edu/bioinf-core/tools
I personally big fan of open source software. You can find link of several open source bioinformatics software at University of North Carolina website.
Link @ http://bioinformatics.unc.edu/software/opensource/
Hi all,
Nice collection of software links. It looks you all are big fan of open source software as well. Please read this Standford University report which outlines recent activity in open source software development within the discipline of bioinformatics.
Link @ http://bmir.stanford.edu/file_asset/index.php/88/
this following weblink also useful:
https://sites.google.com/site/seqomics/sequencing/info-seq/link-seq
List of open source bioinformatics software:
http://www.gmod.org/wiki/Main_Page
If you are interested in code, check out this: http://gmod.org/wiki/GSoC#Project_Ideas
Insight Segmentation and Registration Toolkit (ITK) is an open-source, cross-platform system that provides developers with an extensive suite of software tools for image analysis.
Link @ http://www.itk.org/
Berkeley Bioinformatics Open Source Projects are one of the good resouce for bioinformatician if they are interested in OSS.
Link @ http://www.berkeleybop.org/software
If you are in computer aided drug-design section, this page will be useful for you. http://www.allfordrugs.com/drug-design/
You can find link of the tools and software developed by IIT-D at http://www.scfbio-iitd.res.in/bioinformatics/genefinding.htm
If you are specifically interested in protein based analysis check https://www.scfbio-iitd.res.in/bioinformatics/proteinstructure.htm for some software developed by IIT-D
Are you doing protein based analysis, then please have a look at http://www.imtech.res.in/bic/index.php?option=com_content&view=article&id=46for some of the good servers.
Hey all very nice collection of software and tools collections. I would like you all to redirect Raghava lab page http://www.imtech.res.in/raghava/ for more.
EpiExplorer is a web tool that allows you to use large reference epigenome datasets for your own analysis without complex scripting or laborous preprocessing. http://epiexplorer.mpi-inf.mpg.de/
Qlucore Omics Explorer is a next-generation bioinformatics software program that delivers immediate results. Combine visualization with powerful statistical methods in the easy to use program to obtain new results faster. http://www.qlucore.com/
SAMtool quick tutorial at http://davetang.org/wiki/tiki-index.php?page=SAMTools
http://samtools.sourceforge.net/samtools.shtml
TopHat http://tophat.cbcb.umd.edu/manual.shtml is a program that aligns RNA-Seq reads to a genome in order to identify exon-exon splice junctions. It is built on the ultrafast short read mapping program Bowtie.
This wiki link http://seqanswers.com/wiki/Software/list also provide a comprehensive list of bioinformatics tools.
Bioinformatics NGS tool resources https://wiki.nbic.nl/index.php/NGS_Tools
There are different ways to perform exome sequence analysis, but GATK have a good guide for 'Best Practice': http://www.broadinstitute.org/gatk/guide/best-practices
skewer (transferred from https://sourceforge.net/projects/skewer) implements the bit-masked k-difference matching algorithm dedicated to the task of adapter trimming and it is specially designed for processing next-generation sequencing (NGS) paired-end sequences.
https://github.com/relipmoc/skewer
A program for annotating and predicting the effects of single nucleotide polymorphisms (SNP) http://snpeff.sourceforge.net/
http://snpeff.sourceforge.net/SnpEff_paper.pdf
Tools for next-generation sequencing analysis:
http://ngsutils.org
ARYANA: Aligning Reads by Yet Another Approach http://www.biomedcentral.com/1471-2105/15/S9/S12/abstract