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• • Rahul Agarwal@raag

  

  World of Omics

  By Rahul Agarwal 4176 days ago Comments (5)

  • Omics
  • Sequencing

  How many variants of "omics" techniques presently in use ?

• • Rahul Nayak@rahul

  

  Alignment of closely related whole genomes/scaffolds

  By Rahul Nayak 3249 days ago Comments (1)

  • Whole genome
  • NGS
  • Genome
  • Scaffolds
  • pan-genome
  • Evolution
  • Alignments
  • Compare

  www.cs.utoronto.ca - With the relative ease and low cost of current generation sequencing technologies has led to a dramatic increase in the number of sequenced genomes for species across the tree of life. This increasing volume of data requires tools that can quickly...
• • Rahul Nayak@rahul

  

  BioScripts

  By Rahul Nayak 3464 days ago

  • Bioinformatics
  • Computational Biology
  • Education
  • Solution
  • Study
  • Script
  • Perl
  • Python
  • R
  • Code

  code.google.com - You are requested to please bookmark collection of bioinformatics tools, scripts, codes that can be pieced together in a very easy and flexible manner to perform both simple and complex bioinformatics tasks. The next-generation sequencing included...
• • Martin Jones@martin

  

  Orione – a web-based framework for NGS analysis in microbiology

  By Martin Jones 3804 days ago

  • Bioinformatics
  • Computational Biology
  • NGS
  • Orione
  • Microbiology
  • Visualization

  http://orione.crs4.it/ - End-to-end NGS microbiology data analysis requires a diversity of tools covering bacterial resequencing, de novo assembly, scaffolding, bacterial RNA-Seq, gene annotation and metagenomics. However, the construction of computational pipelines that...
• • Neel@neelam

  

  Integrative Genomics Viewer (IGV) tutorial

  By Neel 3815 days ago

  • Bioinformatics
  • Computational Biology
  • NGS
  • IGV
  • Visualization
  • Tutorial

  wikis.utexas.edu - The Integrative Genomics Viewer (IGV) from the Broad Center allows you to view several types of data files involved in any NGS analysis that employs a reference genome, including how reads from a dataset are mapped, gene annotations, and predicted...
• • Abhimanyu Singh@abhimanyu

  

  Next generation sequencing(NGS) books

  By Abhimanyu Singh 3858 days ago Comments (1)

  • NGS
  • Pipeline
  • Method
  • Books
  • Tutorial

  en.wikibooks.org - Employing different technologies, the purpose of NGS platform is to decode the identity or modification on the nucleotides. NGS platforms evolve quickly and capture the main stream. This bookmark is created to provide NGS online books links.
• • Rahul Agarwal@raag

  

  New RNA Seq tool

  By Rahul Agarwal 3893 days ago Comments (4)

  • Sequencing
  • RNA-Seq

  www.genengnews.com - "By removing the time-consuming step of read mapping, the authors reported, Sailfish able to provide quantification estimates 20–30 times faster than current methods without loss of accuracy." Tool...

No files.

• • LEGE@lege

  

  LEGE commented on a bookmark Next Generation Sequencing (NGS) Tutorials 1804 days ago

  Informatics for RNA-seq: A web resource for analysis on the cloud https://github.com/griffithlab/rnaseq_tutorial?
• • Rahul Nayak@rahul

  

  Rahul Nayak replied on the discussion topic Want to Know which genome assembler rule the world ? 2180 days ago

  Canu Assembler is my personal favourate.Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequelor Oxford Nanopore MinION).
• • BioStar@biostar

  

  BioStar replied on the discussion topic Want to Know which genome assembler rule the world ? 2295 days ago

  Genome assembly tools at https://bioinformaticsonline.com/search?q=assembly&entity_type=object&entity_subtype=bookmarks&offset=0&search_type=entities
• • Priya Singh@priyasingh

  

  Priya Singh replied on the discussion topic Does anyone have Nanopore latest updates? 2782 days ago

  92% genome coverage of E. coli, average depth of 3.8x. But from just _43_ reads https://github.com/nickloman/massive-nanopore-silliness http://lab.loman.net/2017/03/09/ultrareads-for-nanopore/

• • Poonam Mahapatra@poonam

  

  Does anyone have Nanopore latest updates?

  Started by Poonam Mahapatra 4149 days ago Replies (34) Last reply by Priya Singh 2782 days ago

  • NGS
  • Sequencing
  • Oxford Nanopore
  • Medicine
  • Sequencing Technology

  There was a lot of buzz about Oxford Nanopore Technologies® is developing the GridION™ system and miniaturised MinION™ device. These are a new generation of electronic molecular analysis system for use in scientific research,...
• • Rahul Agarwal@raag

  

  Want to Know which genome assembler rule the world ?

  Started by Rahul Agarwal 4150 days ago Replies (3) Last reply by Rahul Nayak 2180 days ago

  • Sequencing
  • DNA
  • Genome Assembly
  • Assembler
  • Omics
  • de novo

  Assemblathon 2: evaluating de novo methods of genome...
• • Rahul Agarwal@raag

  

  Compressive Genomics

  Started by Rahul Agarwal 4150 days ago

  • data compression
  • genomics
  • sequencing
  • redundancy
  • repeats
  • bam
  • sff
  • gz
  • zip

  The key to finding a solution is to notice that most genomicsequences differ by very little. It may well be that the number of complete genome sequences being stored is increasing rapidly, but the actual amount of new data is very small. In...
• • Rahul Agarwal@raag

  

  Is reference genome necessary for gene expression study in transcriptome sequencing or for variant...

  Started by Rahul Agarwal 4175 days ago

  • Sequencing
  • RNA
  • DNA
  • Genome

  Like in case of plant genomes where nature of genome is too complex and huge in size to accomplish complete de novo assembly by current sequencing technology. What would be alternate solution? Can we live in reference free world?

• 

  Software packages for next gen sequence analysis

  Last updated 3473 days ago by Rahul Nayak Comments (5)

  • Bioinformatics
  • Computational Biology
  • Education
  • Assemblied
  • Sequence
  • Genome
  • Align
  • Software
  • SNP

  Integrated solutions * CLCbio Genomics Workbench - de novo and reference assembly of Sanger, Roche FLX, Illumina, Helicos, and SOLiD data. Commercial next-gen-seq software that extends the CLCbio Main Workbench software. Includes SNP detection,...
• 

  Commercial and public next-gen-seq (NGS) software

  Last updated 3749 days ago by Partek Comments (7)

  • Bioinformatics
  • Computational Biology
  • NGS
  • Next generation sequencing
  • Tools
  • Software
  • SNP
  • Assembly
  • Pipeline

  Integrated solutions CLCbio Genomics Workbench - de novo and reference assembly of Sanger, Roche FLX, Illumina, Helicos, and SOLiD data. Commercial next-gen-seq software that extends the CLCbio Main Workbench software. Includes SNP detection,...
• 

  Useful Publications and Websites for Deep Sequencing Data Analysis

  Last updated 4010 days ago by Rahul Nayak

  • Bioinformatics
  • Genomics
  • NGS
  • Deep Sequencing

  Global overview papers Next generation quantitative genetics in plants. Jiménez-Gómez, Frontiers in Plant Science 2:77, 2011 Full Text [equally relevant to animal and microbial systems] Sense from sequence reads: methods for...
• 

  Genome Browsers

  Last updated 4145 days ago by Rahul Agarwal Comments (2)

  • Genome Browser
  • Organism
  • Plant
  • Animal
  • Bacteria
  • fungi
  • Genome Sequence
  • DNA
  • Sequencing
  • Annotation
  • SNP
  • gff
  • gtf
  • gff3
  • vcf
  • bed

  Genome Browser is the platform/database used for searching and retreiving sequences and annotation of genomes belong to various eukaryotes, prokaryotes, etc. Following are the weblink for different available...
• 

  Structure of Binary files used for storing sequencing data-bam and sff

  Last updated 4150 days ago by Rahul Agarwal

  • bam
  • sff
  • sam
  • iontorrent data
  • 454 data
  • pyrosequencing data
  • hxd
  • hexadecimal
  • binary files
  • sequencing

  Many times bioinformatician needs to parse binary files like bam and sff. Advantage of binary files is that they occupy less space in memory with maximum information content. Link for those who looking for structure of Bam and sff...

• • Jitendra Narayan@admin

  

  Sequencing By Xpansion

  By Jitendra Narayan 3475 days ago

  • Bioinformatics
  • Computational Biology
  • Education
  • Sequence
  • Seq
  • Genome
  • Xpansion

  Xpandomer in a single drop reaction to sequence an entire human genome 1000X over.
• • Martin Jones@martin

  

  deepTools

  By Martin Jones 3696 days ago

  • Bioinformatics
  • Computational Biology
  • NGS
  • deepTools
  • Genome
  • RNA-Seq
  • Visualization
  • Tools

  User-friendly tools for the normalization and visualization of deep-sequencing data
• • Rahul Agarwal@raag

  

  Drawback of Exome Sequencing

  By Rahul Agarwal 3855 days ago

  • Exome
  • WGS
  • Sequencing
  • Clinical
  • omics
  • diagnostics

  Smaller Exome datasets were found to be worse performer than those from larger datasets (WGS)
• • Madhvan Reddy@madhvan

  

  The genome factory !!!

  By Madhvan Reddy 3992 days ago

  • Bioinformatics
  • Genomics
  • NGS
  • Deep Sequencing

  World’s first $1,000 genome enables ‘factory’ scale sequencing for population and disease studies

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