Useful Publications and Websites for Deep Sequencing Data Analysis
...ent de novo assembly of large genomes using compressed data struct...software package] Comparing genomes and assemblies; variant dete...High-throughput genotyping by whole-genome resequencing. Huang et...ty of California - Santa Cruz Genome Browser is on the FAQ list...3786 days ago
List of bioinformatics open source projects/software.
Open source software is software that can be freely used, changed, and shared...information about biological sequences collected from the environment. GenomeSpace http://www.genomespace.org/ Centralized web ap...3764 days ago
List of generic simulation software/tools/resource with brief description and homepage !!!
...ts/gametes/?source=navbarGASP Genometric Analysis Simulation Progr...NOME A rapid coalescent-based whole genome simulator http://www.sp...s/gensim/GWAsimulator A rapid whole genome simulation program http...al composition of typical metagenome data sets http://ab.inf.uni-t...3744 days ago
Next generation sequencing in R or bioconductor environment
There are many R software and bioconductor...s, rtracklayer, GenomicFeatures and BSgenome. Compared to the IRange...for SNP analysis: snpMatrix BSgenome BSgenome provides an object...s the biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest and stat pac...3632 days ago
Commercial and public next-gen-seq (NGS) software
...modular system for the rapid whole genome alignment of finished o...na reads to a FASTA reference genome. By Andrew D. Smith and Zheny...ALLPATHS: De novo assembly of whole-genome shotgun microreads. ALL...zner from UCSD. (published in Genome Research)RMAP (A program for...3526 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-annotations-by-position/ htt...3556 days ago
Apps for Busy Bioinformatics Researchers !!!
...p/geneindex/id319769866?mt=8 Genome Voyager: iPad Gain first ha...sease by analyzing cases with whole genome sequencing data that ha...arning purposes. Visualize whole human genome sequencing data i...ne alsocontains an integrated genome browser with information on g...3548 days ago
List of Biotechnology Research Laboratory, University, and Centre in India
DEPARTMENT OF BIOTECHNOLOGY Centre For DNA Fingerprinting And Diagnostics (CDFD),...swar National Institute Of Immunology, New Delhi National Centre For Plant Genome Research (NCPGR), JNU, New De...2578 days ago
Software packages for next gen sequence analysis
...ment of Nucleotide Databases. Whole genome alignments to a reference gen...na reads to a FASTA reference genome. By Andrew D. Smith and Zheny...ALLPATHS: De novo assembly of whole-genome shotgun microreads. ALL...om the Canada's Michael Smith Genome Sciences Centre. Perl/Linux....3249 days ago
Comprehensive list of visualization tools for biological pathways
The study of biological pathways is a key to understand the different process....kazusa.or.jp/ KEGG Atlas Interactive Kyoto Encyclopedia of Genes and Genomes pathways http://www.genome.jp/kegg/ Omix Visuali...2294 days ago