Results for "Assembly"
Users
About me: I am a bioinformatician, working as a SRF fellow. Working on Shotgun Assembly database.1176 days ago
- About me: ...ng technologies like shotgun sequencing, linked reads, and long-read sequencing for whole-genome resequencing, variant calling, and transcriptome assembly, and differential expression...
1169 days ago
Blogs
Five points for bioinformatics software/tools
...ot absolve you of the need to actually read and research the type of analysis that you are doing. This is particularly true in the case of genome assembly and annotation. At the end,...3737 days ago
Dynamic chromosome breakpoints !!!
...yribonucleic acid (DNA) goes through a condensation and decondensation process. This is followed by nuclear envelope dissolution, mitotic spindle assembly, migration of the sister chro...3582 days ago
- +13 more Blogs
Bookmarks
Comparison of Short Read De Novo Alignment Algorithms
Excellent article to introduce different sequencing methods along with tools for de novo assembly of sequencing reads and their relevant references. Title: Comparison of Short Read De Novo Alignment Algorithms Author: Nikhil Gopal3939 days ago
Next Generation Sequencing (NGS) Tutorials
...Variant Detection Introductory tutorial https://docs.google.com/document/pub?id=1ZRzrjjOCvtAu3m-IKL-rbJ1f4On60dDL_IEwG7oejdI Microbial de novo Assembly for Illumina Data Introductor...3517 days ago
- +249 more Bookmarks
Files
Bioinformatics approach to Boar Taint
...in Illumina HiSeq2000 to >10X average coverage. Short reads generated from these samples mapped to Sus Scrofa version 10.2 reference assembly using Bowtie2. Alignment file...3819 days ago
- Saved Cornell University assembly workshop PPT. Reference: http://cbsu.tc.cornell.edu/lab/doc/assembly_workshop_20150420_lecture1.pdf
2827 days ago
- +2 more Files
Discussion topics
- 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?
3974 days ago
Want to Know which genome assembler rule the world ?
Assemblathon 2: evaluating de novo methods of genome assembly http://www.gigasciencejournal.com/content/2/1/10/abstract http://blogs.nature.com/news/2013/07/genome-assembly-contest-prompts-soul-searchin...3949 days ago
Pages
Bio++ : C Language libraries for your biological need
...to many machine-level features that would otherwise require the use of Assembly Language. As Dennis Ritchie...need for a system implementation language efficient enough to displace assembly language, yet sufficiently ab...3977 days ago
Genome Assembly Tools and Software - PART2 !!
...s and it rteturns an improved assembly (more contiguous and more cor...and removes them prior to the assembly. The established software Phr...nbsp;is a method for accurate assembly of a heterogeneous viral popu...o use for your Velvet de novo assembly. It needs two inputs: the est...2715 days ago
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Top-level pages
- ...t al. (2001) The sequence of the human genome. Science 291:1304–1351R.D. Fleischmann et al. (1995) Whole–genome random sequencing and assembly of haemophilus–influenz...
3977 days ago
- ...short mRNA sequence, and complex submissio Staden The Staden Package consists of a series of tools for DNA sequence preparation (pregap4), assembly (gap4), editing (gap4) and DN...
3971 days ago
- +19 more Top-level pages
Wire posts
News
- ...ers, Scalpel works by performing de novo assembly of regions of interest, so th...alpel's innovation is to repeatedly check its assembly before comparing to the refer...s are eliminated. This ensures that the final assembly of the exon is highly accurat...
3576 days ago
- ...ce, Aedes aegypti, and Ixodes scapularis Whole genome alignments for O. longistaminata and T. cacao Non-coding RNA gene models in Bacteria New assembly of tomato (version 2.50) Ful...
3275 days ago
- +6 more News
Opportunity posts
Bioinformatics JRF/SRF position at IARI
...ence in proteomics, genomics and structural biology. Knowledge of programming language, perl and database – HTML, CSS, Java script. NGS sequence assembly and analysis and algorithm de...3561 days ago
Postgraduate Research Associate Bioinformatics / Computational Biology (Reference code: 59)
...beet (Dohm et al., Nature, 2014), a crop plant closely related to quinoa (same family, but different genus). Not yet published is a quinoa genome assembly that we have generated, and w...3226 days ago
- +13 more Opportunity posts
ResearchLabs posts
- ...the compound-efflux system interactions Action of inhibitors on efflux systems Structural and dynamical features of the efflux systems TatA Assembly of the TatA system Study of...
3898 days ago
- ...analysis of the read depth-of-coverage; (iii) split read analysis, which detects SVs by evaluating gapped sequence alignments; and (iv) sequence assembly, which enables the discovery...
3022 days ago
- +2 more ResearchLabs posts
Video
How DNA is Packaged (Advanced)
...CRIPT: In this animation we'll see the remarkable way our DNA is tightly packed up to fit into the nucleus of every cell. The process starts with assembly of a nucleosome, which is for...3906 days ago
Bio-Scripts
Download the genome from NCBI using bash script/command
...cd genome # Look for genome assembly summary and extract the URL...nlm.nih.gov/genomes/refseq/fungi/assembly_summary.txt' | awk '{FS="\t"}...nih.gov/genomes/genbank/bacteria/assembly_summary.txt' | awk '{FS="\t"}....nih.gov/genomes/refseq/protozoa/assembly_summary.txt' | awk '{FS="\t"}...2561 days ago
Download the gff files from NCBI using bash script/command
...genome_gff # Look for genome assembly summary and extract the URL...nlm.nih.gov/genomes/refseq/fungi/assembly_summary.txt' | awk '{FS="\t"}...nih.gov/genomes/genbank/bacteria/assembly_summary.txt' | awk '{FS="\t"}....nih.gov/genomes/refseq/protozoa/assembly_summary.txt' | awk '{FS="\t"}...2552 days ago
- +22 more Bio-Scripts
Polls
Which of the following programming language is best for a bioinformatics beginner?
...rk and I will like to learn a programming language which is compatible with most bioinformatics tools or software. I basically want to do de-novo assembly, map reads, align reads, and...3560 days ago
Groups
...H data Probabilistic graphical models Gibbs sampling for motif finding Biclustering algorithms Genome Assembly Developement of new algorithms to speed up the assembly procedure Comparative genomi...3972 days ago
Tags
- https://genome10k.soe.ucsc.edu The Genome 10K project aims to assemble a genomic zoo—a collection of DNA sequences representing the genomes of 10,000 vertebrate species, approximately one for every vertebrate genus. The trajectory of cost reduction in DNA sequencing suggests that this project wi...
Tags: Bioinformatics, Computational Biology, Genetics, Sequencing, G10K, Variant, Assembly, Animal
3597 days ago
Comments
Comment on "Short-read assembly using Spades !"
...software tool for short-read assembly. Here are the general steps for short-read assembly using SPAdes: Quality co...TQ format. Evaluation of assembly: After running SPAdes, the ne...repeated until a satisfactory assembly is achieved. These are t...445 days ago
Comment on "Short-read assembly using Spades !"
...e assembler) is a popular tool for short-read assembly. It can assemble reads genera...overview of how to use SPAdes for short-read assembly: Install SPAdes: SPAdes...also provides several options for tuning the assembly parameters, such as adjusting...450 days ago
- +41 more Comments
