Results for "Assembly"
Users
About me: I am a bioinformatician, working as a SRF fellow. Working on Shotgun Assembly database.1137 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...
1130 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,...3698 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...3543 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 Gopal3900 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...3478 days ago
- +247 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...3780 days ago
- Saved Cornell University assembly workshop PPT. Reference: http://cbsu.tc.cornell.edu/lab/doc/assembly_workshop_20150420_lecture1.pdf
2788 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?
3935 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...3910 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...3938 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...2676 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...
3938 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...
3932 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...
3537 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...
3236 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...3522 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...3187 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...
3859 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...
2983 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...3867 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"}...2522 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"}...2513 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...3521 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...3933 days ago
Tags
- When you have both Illumina and Nanopore data, then SPAdes remains a good option for hybrid assembly - SPAdes was used to produce the B fragilis assembly by Mick Watson’s group. Again, running spades.py will show you the options: spades.py This produces: SPAdes genome ...
Tags: SPAdes, hybrid, genome, assembly, ONT, Nanopore
2341 days ago
Short-read assembly using Spades !
If we only had Illumina reads, we could also assemble these using the tool Spades. You can try this here, or try it later on your own data. Get data We will use the same Illumina data as we used above: illumina_R1.fastq.gz: the Illumina forward reads illumina_R2.fastq.gz: the Illumina reve...Tags: spades, assembly, short, reads, genome, tools
815 days ago
- +4 more Tags
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...406 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...411 days ago
- +41 more Comments
