Results for "de novo"
Blogs
Software and Tools to detect structure variation with long reads !!
...tion between genetics and heritable diseases requires an approach that looks at all the variant bases and types in a genome. While a PacBio de novo assembly resolves the mo...2598 days ago
String graph based genome assembly software and tools !
...embly of GEnomes https://github.com/lucian-ilie/SAGE2 SAGE, for de novo genome assembly. As opposed t...olding. 5. Fermi https://github.com/lh3/fermi/ Fermi is a de novo assembler with a particular f...2318 days ago
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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
...idPKLxM Variant Detection Introductory tutorial https://docs.google.com/document/pub?id=1ZRzrjjOCvtAu3m-IKL-rbJ1f4On60dDL_IEwG7oejdI Microbial de novo Assembly for Illumina Data In...3477 days ago
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Files
Evaluation of genome assembly software based on long reads
TGS technologies have been used to produce highly accurate de novo assemblies of hundreds of microbial geno...re: Celera Assembler , Falcon , Miniasm, Newbler , SGA Assembler, Smartdenovo, Abruijn, Ra, DBG2OLC, Spades...1910 days ago
- SPAdes—St. Petersburg genome Assembler—was originally developed for de novo assembly of genome sequencing data produced for cultivated microbial isolates and for single-c...
814 days ago
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?
3934 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-c...3910 days ago
Pages
Genome Assembly Tools and Software - PART2 !!
...e that GeneStitch support is SOAPdenovo. RACA 0.9.1.1 – Refere...ent reads. SeqCons 1.0 – de novo and reference-guided Sequence...new string-overlap graph-based de novo genome assembler. Omega 1.0....emblies. Fermi 1.1 – WGS de novo Assembler based on the FMD-in...2675 days ago
Awesome perl frameworks, libraries and software - PART 4
...th signatures, no source filter yogan/cope - A colourful wrapper for terminal programs trinityrnaseq/trinityrnaseq - Trinity RNA-Seq de novo transcriptome assembly tokuh...2484 days ago
Top-level pages
Bioinformatics Companies in India
...o Park, Basavangudi, Bangalore – 4www.molecularconnections.com 22.Novo Informatics Pvt. Ltd.TBIU, 2n...lhi-16.Contact: 91-11-26581524, 91-11-26581766(Extension: 28)Email: info@novoinformatics.comwww.novoinforma...3915 days ago
Useful Publications and Websites for Deep Sequencing Data Analysis
...t al., Bioinformatics 27(13):i137-41, 2011. PubMedCentral De novo assembly Velvet: algorithms for de novo short read assembly using de...Full Text Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping...3769 days ago
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Wire posts
News
Accelerating Biology 2014:The Next Wave (18-22 February, 2014)
...r cost. The availability of hundreds of genomes in a short time is expected to revolutionize area of life sciences. A number of new methods like de-novo sequencing, resequencing, tra...3835 days ago
- ...HaplotypeCaller and SOAPindel in test runs on both simulated and real whole human exomes. Like other indel callers, Scalpel works by performing de novo assembly of regions of i...
3536 days ago
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Opportunity posts
- ...is of different file formats and their conversions. 2. Assessing the quality of data and filtering of raw reads. 3. Assembling the raw reads-de novo as well as reference mapping...
3633 days ago
JRF in Bioinformatics @ Bioinformatics Centre, North-Eastern Hill University
Applications with complete bio-data are invited for JRF (3) and Project Assistant (1) in a DBT project "Next Generation Sequencing (NGS)-based de novo assembly of expressed transcrip...3458 days ago
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Bio-Scripts
- ...░▓▓▓^▓▓▓░ Transrate v1.0.3 by Richard Smith-Unna, Chris Boursnell, Rob Patro, Julian Hibberd, and Steve Kelly DESCRIPTION: Analyse a de-novo transcriptome assembly using...
2113 days ago
Pack a perl program with their dependencies on Ubuntu !
...BioStar 409 days ago Evaluationgenomeassemblysoftwarelongreads TGS technologies have been used to produce highly accurate de novo assemblies of hundreds of mic...1501 days ago
Polls
Which of the following programming language is best for a bioinformatics beginner?
...arch work 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 re...3520 days ago
Tags
- Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences of highly heterozygous diploids from massively parallel shotgun sequencing data. The latest version is 1.2.4. To cite Platanus, please use the following: Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y,...
Tags: Bioinformatics, NGS, Assembly, de novo, Sequence, Assembler, Heterozygous
2904 days ago
miniasm: very fast OLC-based de novo assembler for noisy long reads
Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream assemblers, miniasm does not have a consensus step. I...Tags: Ultrafast, de novo, assembly, long, noisy, reads, consensus
2341 days ago
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Comments
- ...-Chain is a package of quality control tools for next generation sequencing (NGS) data, consisting of both raw reads quality evaluation and de novo contamination screening, whic...
2127 days ago
- Canu is one of the best de novo assemblers available for long reads - it’s a fork and updated version of the Celera assembler that was used to assemble the human genome....
2165 days ago
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