Results for "NGS"
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Most variant calling pipelines result in files containing large quantities of variant information. The variant call format (vcf) is an increasingly popular format for this data. The format of these files and their content is discussed in the vignette ‘vcf data.’ These files ...Tags: Bioinformatics, Analysis, NGS, vcfR, R, Visualization, VCF, Genome
2843 days ago
- Faster, more accurate algorithms function prediction "GeneMANIA (Multiple Association Network Integration Algorithm)" have however been developed in recent years and are publicly available on the web, indicating the future direction of function prediction.
Tags: Bioinformatics, Analysis, NGS, Annotation, Genome
2840 days ago
- Recent technological progress has greatly facilitated de novo genome sequencing. However, de novo assemblies consist in many pieces of contiguous sequence (contigs) arranged in thousands of scaffolds instead of small numbers of chromosomes. Confirming and improving the quality...
Tags: Bioinformatics, Analysis, NGS, Stats, Assemble, Plot, TGNet, Visualize, Genome
2838 days ago
- A probabilistic framework for structural variant discovery. Ryan M Layer, Colby Chiang, Aaron R Quinlan, and Ira M Hall. 2014. "LUMPY: a Probabilistic Framework for Structural Variant Discovery." Genome Biology 15 (6): R84. doi:10.1186/gb-2014-15-6-r84. More at https://github.com/arq5...
Tags: Bioinformatics, Analysis, NGS, Lumpy, SV, Variation, Structure, Genome
2837 days ago
- I am working on assembly of new genome. I am just wondering how to validate my assembled genome?
Tags: Bioinformatics, NGS, Assembly, Validate, Approach, Tools
2824 days ago
GeneValidator - Identify problems with predicted genes
GeneValidator helps in identifing problems with gene predictions and provide useful information extracted from analysing orthologs in BLAST databases. The results produced can be used by biocurators and researchers who need accurate gene predictions. If you would like to use GeneValidator on a f...Tags: Bioinformatics, Analysis, NGS, Gene, Prediction, GeneValidator, Genome
2836 days ago
- In this exercise, a previously annotated gene will be used to measure the accuracy of different gene finding approaches. GRAIL, GENSCAN, geneid, FGENESH, GenomeScan, GrailEXP and GENEWISE will be used to annotate the sequence. Both search by signal, content and homology (protein and cDNA seq...
Tags: Bioinformatics, Analysis, NGS, Gene, Prediction, Finding, Genome
2836 days ago
- Collections of few handy tools for bioinformatician http://molbiol-tools.ca/Convert.htm
Tags: Bioinformatics, Analysis, NGS, Tools, Gene, Genome, Format
2833 days ago
- gKaKs is a codon-based genome-level Ka/Ks computation pipeline developed and based on programs from four widely used packages: BLAT, BLASTALL (including bl2seq, formatdb and fastacmd), PAML (including codeml and yn00) and KaKs_Calculator (including 10 substitution rate estimation methods). gKaKs ...
Tags: Bioinformatics, Analysis, NGS, Ka, Ks and Ka/Ks, calculations, Genome
2833 days ago
