BOL: List of popular bioinformatics software/tools

List of popular bioinformatics software/tools

Jitendra Narayan — Tue, 16 Jul 2013 14:30:30 -0500

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.

Address of the bookmark: http://samtools.sourceforge.net/swlist.shtml

Comment by Jit

Jit — Fri, 19 Feb 2016 08:53:23 -0600

MEDIPS: genome-wide dierential coverage analysis of sequencing

MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments https://www.bioconductor.org/packages/3.3/bioc/vignettes/MEDIPS/inst/doc/MEDIPS.pdf

Comment by Rahul Nayak

Rahul Nayak — Sun, 07 Feb 2016 14:13:08 -0600

Mapping single molecule sequencing reads using Basic Local Alignment with Successive Refinement (BLASR) http://bix.ucsd.edu/projects/blasr/

Comment by Priya Singh

Priya Singh — Tue, 12 Jan 2016 02:40:43 -0600

PLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, such as the Blast suite of algorithms.

Relying on unique software architecture, PLAST takes full advantage of recent multi-core personal computers without requiring any additional hardware devices.

More at https://plast.inria.fr/

Comment by Abhimanyu Singh

Abhimanyu Singh — Fri, 12 Sep 2014 00:41:17 -0500

ARYANA: Aligning Reads by Yet Another Approach http://www.biomedcentral.com/1471-2105/15/S9/S12/abstract

Comment by Rahul Agarwal

Rahul Agarwal — Sat, 26 Jul 2014 16:57:05 -0500

Tools for next-generation sequencing analysis:

http://ngsutils.org

Comment by Jit

Jit — Sat, 26 Jul 2014 06:54:03 -0500

A program for annotating and predicting the effects of single nucleotide polymorphisms (SNP) http://snpeff.sourceforge.net/

http://snpeff.sourceforge.net/SnpEff_paper.pdf

Comment by Martin Jones

Martin Jones — Fri, 25 Jul 2014 02:07:53 -0500

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

Comment by John Parker

John Parker — Wed, 09 Jul 2014 04:56:19 -0500

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

Comment by Rahul Nayak

Rahul Nayak — Sun, 08 Jun 2014 16:32:18 -0500

Bioinformatics NGS tool resources https://wiki.nbic.nl/index.php/NGS_Tools

Comment by Abhimanyu Singh

Abhimanyu Singh — Fri, 30 May 2014 04:55:22 -0500

This wiki link http://seqanswers.com/wiki/Software/list also provide a comprehensive list of bioinformatics tools.

Comment by Rahul Nayak

Rahul Nayak — Sat, 10 May 2014 04:37:47 -0500

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.

Comment by Prachi Taneja

Prachi Taneja — Sat, 10 May 2014 04:20:46 -0500

SAMtool quick tutorial at http://davetang.org/wiki/tiki-index.php?page=SAMTools

http://samtools.sourceforge.net/samtools.shtml

Comment by Rahul Nayak

Rahul Nayak — Sun, 06 Apr 2014 19:35:57 -0500

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/

Comment by Rahul Nayak

Rahul Nayak — Sun, 06 Apr 2014 19:31:56 -0500

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/

Comment by Archana Malhotra

Archana Malhotra — Fri, 09 Aug 2013 14:55:02 -0500

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.

Comment by Jitendra Narayan

Jitendra Narayan — Fri, 09 Aug 2013 14:32:08 -0500

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.

Comment by Jit

Jit — Fri, 09 Aug 2013 14:24:58 -0500

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

Comment by Jit

Jit — Fri, 09 Aug 2013 14:23:26 -0500

You can find link of the tools and software developed by IIT-D at http://www.scfbio-iitd.res.in/bioinformatics/genefinding.htm

Comment by Manshi Raghubanshi

Manshi Raghubanshi — Thu, 01 Aug 2013 17:33:01 -0500

If you are in computer aided drug-design section, this page will be useful for you. http://www.allfordrugs.com/drug-design/

Comment by Jitendra Narayan

Jitendra Narayan — Fri, 19 Jul 2013 10:35:48 -0500

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

Comment by Jitendra Narayan

Jitendra Narayan — Fri, 19 Jul 2013 10:32:50 -0500

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/

Comment by Jit

Jit — Fri, 19 Jul 2013 10:29:41 -0500

If you are interested in code, check out this: http://gmod.org/wiki/GSoC#Project_Ideas

Comment by Jit

Jit — Fri, 19 Jul 2013 10:28:00 -0500

List of open source bioinformatics software:

http://www.gmod.org/wiki/Main_Page

Comment by Rahul Agarwal

Rahul Agarwal — Tue, 16 Jul 2013 16:00:03 -0500

this following weblink also useful:

https://sites.google.com/site/seqomics/sequencing/info-seq/link-seq

Comment by Jitendra Prajapati

Jitendra Prajapati — Tue, 16 Jul 2013 15:51:39 -0500

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/