Results for "Variant"
Users
About me: ...d in using next-generation sequencing technologies like shotgun sequencing, linked reads, and long-read sequencing for whole-genome resequencing, variant calling, and transcriptome as...Skills: Variant Calling1138 days ago
Blogs
Computer simulation of genetic mechanism !!
...w.uhnresearch.ca/labs/tillier/software.htm#3 SimRare Rare variant simulation and analysis tool...for the simulation of the introduction and evolution of (rare) genetic variants. http://simupop.sourceforge....2973 days ago
Structural variation: the hidden genomic treasure
... The most‐studied structural variants are copy number variations (...consequences. Structural variants (SVs) such as deletions, ins...of new detection methods, smaller variants (between 50 and 1000 base pa...iscovery of unbalanced structural variants (copy-number variants) with...2701 days ago
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Bookmarks
DAVI: Deep learning-based tool for alignment and single nucleotide variant identification
DAVI consists of models for both global and local alignment and for variant calling. We have evaluated the performance of DAVI against existing state-of-the-art tool sets and found th...1144 days ago
Next Generation Sequencing (NGS) Tutorials
...ww.isb-sib.ch/training/training-activities-schedule/archive-2013.html Variant Detection (Model organism) Ad...ogle.com/document/pub?id=1CuKkKylVDb03tnN7RSWl5EUzleetn0ctjmvaidPKLxM Variant Detection Introductory tutori...3486 days ago
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Files
Bioinformatics approach to Boar Taint
...steroids which is objectionable to many consumers. Detected functional variant(s) underlying boar taint comp...identified QTL regions on SSC5,13, and 7 with the aid of FreeBayes , a variant caller tool. A final list of...3788 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?
3943 days ago
Pages
Genome Assembly Tools and Software - PART2 !!
...reads in a SAM file and a set of variant calls in VCF format, HAPCOMPA...ash; Genome Shotgun Assembler and Variant CallerDISCOVAR is a whol...tection and Assembly of Insertion VariantsMindTheGap is a software...a simple error correction, viral variants assembling based on maximum-...2684 days ago
Top-level pages
- ...r phase by merging them.The binary search algorithm is an example of a variant of divide and conquer called...irected graphs, notably by using the simplex algorithm. A complex variant of linear programming is call...
3944 days ago
Useful Publications and Websites for Deep Sequencing Data Analysis
...escribes the RSEM software package] Comparing genomes and assemblies; variant detection Versatile and ope...ata. Krawitz et al, Bioinformatics 26(6):722-9, 2010. Full Text vipR: variant identification in pooled DNA...3778 days ago
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Wire posts
News
Roche has acquired Bina Technologies !!!
...mpany based in California. The biotech’s first product was the Bina Box, a platform for secondary genomic analysis, sequence alignment, and variant calling, but since 2012, it h...3412 days ago
Webinar on 'An integrated RNA and DNA approach to unravel genetic regulation in cancer'
...Mutations in the genome result in diverse transcriptional aberrations that can be missed in a stand-alone WES/WGS analysis. An integration of DNA variant analysis and RNA-Seq analysis...3369 days ago
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Opportunity posts
Human Genome Meeting 2014, Geneva, Switzerland
...the genome sequence of each individual. The biomedical world is now faced with the enormous challenges of assigning pathogenicity to each genomic variant, the functional analysis of t...3878 days ago
Biinformamatics Lead at Google Life Sciences
...in broad kinds of individual and population data. Develop novel platform-level analytical tools for sequence-based assays (assembly, annotation, variant calling and interpretation, p...3487 days ago
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Bio-Scripts
- ...-------------------- Copy Number Variant Discovery:...ad coverage to detect copy number variants. AnnotateIntervals...ted sequencing data. CollectVariantCallingMetrics (Picard)...-------------------------- Short Variant Discovery:...
2073 days ago
- library(vcfR) # Input the files. vcf
2058 days ago
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Tags
Ensembl Variation - Calculated variant consequences
For each variant that is mapped to the reference genome, we identify all overlapping Ensembl transcripts. We then use a rule-based approach to predict the effects that each allele of the variant may have on each transcript. The set of consequence terms, defined by the Sequence Ontology ...Tags: Ensembl, Variation, Calculated, variant, consequences, Variant, Effect, Predictor
2063 days ago
Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data
Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. By using local realignment of reads and local assembly it achieves both high sensitivity and high specificity. Platypus can detect SNPs, MNPs, short indels, replacements and (using th...Tags: Platypus, Haplotype-Based, Variant, Caller, Next, Generation, Sequence, Data, NGS, SNP
2017 days ago
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Comments
Comment on "Coronavirus Resources !"
...oV-2 Interagency Group (SIG) developed a Variant Classification scheme that defines three classes of SARS-CoV-2 variants: Variant of Interest Var...on https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html959 days ago
Comment on "Calling variants in non-diploid systems"
FreeBayes is widely used for calling variants in diploid systems. However, it can also be used for calling variants in pooled samples where the...tion of FreeBayes to generate frequency-based variant calls as well as some other o...1042 days ago
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