Useful Publications and Websites for Deep Sequencing Data Analysis
Global overview papers Next generation quantitative genetics in p...uencing errors. Kelley et al, Genome Biol 11(11):R116, 2010. PubM...ent de novo assembly of large genomes using compressed data struct...software package] Comparing genomes and assemblies; variant dete...3791 days ago
List of bioinformatics open source projects/software.
...ides access to more than 150 genomic analysis tools GeWorkbench http://wiki.c2b2.columbia.edu/workbench/index.php/Home Genomic da...biological sequences collected from the environment. GenomeSpace http://www.genomespace.org/ Centralized web appli...3768 days ago
List of generic simulation software/tools/resource with brief description and homepage !!!
List of generic simulation software/tools/resource with brief desc...LF A Simulation Framework for Genome Evolution http://www.cbrg.eth...on test bed for hypotheses of genome evolution http://acb.qfab.org...ts/gametes/?source=navbarGASP Genometric Analysis Simulation Progr...3749 days ago
Next generation sequencing in R or bioconductor environment
There are many R software and bioconductor packages for NGS data analysis..., rtracklayer, GenomicFeatures and BSgenome. Compared to the IRange...or SNP analysis: snpMatrix BSgenome BSgenome provides an object...the biomaRt, IRanges, Biostrings, BSgenome, G...3636 days ago
Commercial and public next-gen-seq (NGS) software
...uences produced on a Illumina Genome Analyzer. A suite created by..., such as the human reference genome. By default, BWA finds an ali...na reads to a FASTA reference genome. By Andrew D. Smith and Zhenyu X...zner from UCSD. (published in Genome Research)RMAP (A program for map...3530 days ago
Using Interval Trees to Query Genome Annotations by Position
To work on query related to overlapping genomic features: use IntervalTree python pkg http://informatics.malariagen.net/2011/07/07/using-interval-trees-to-query-genome-an...3561 days ago
Apps for Busy Bioinformatics Researchers !!!
DNAApp: DNAApp: for iPhone/iPad This is an iOS app that allows for the...COSMIC, KEGG, PubMed, SymAtlas, UCSC genome browser, Pathway Commons, Gen...m/us/app/geneindex/id319769866?mt=8 Genome Voyager: iPad Gain first han.... SimGene alsocontains an integrated genome br...3553 days ago
List of Biotechnology Research Laboratory, University, and Centre in India
DEPARTMENT OF BIOTECHNOLOGY Centre For DNA Fingerprinting And Diagnostics (CDFD), Hyderabad ( Institute of Bi...war National Institute Of Immunology, New Delhi National Centre For Plant Genome Re...2582 days ago
Software packages for next gen sequence analysis
...uences produced on a Illumina Genome Analyzer. A suite created by...f Nucleotide Databases. Whole genome alignments to a reference gen...na reads to a FASTA reference genome. By Andrew D. Smith and Zhenyu X...om the Canada's Michael Smith Genome Sciences Centre. Perl/Linux. * S...3254 days ago
Comprehensive list of visualization tools for biological pathways
The study of biological pathways is a key to understand the different processes inside a cell: proteins exe...kazusa.or.jp/ KEGG Atlas Interactive Kyoto Encyclopedia of Genes and Genomes pathways http://www.genome.jp...2299 days ago