Results for "Framework"
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Assembly Likelihood Evaluation (ALE) framework that overcomes these limitations, systematically evaluating the accuracy of an assembly in a reference-independent manner using rigorous statistical methods. This framework is comprehensive, and integrates read quality, mate pair orientation and inse...Tags: Bioinformatics, FASTQ, NGS, ALE, Framework, Stats, Reads, Evaluation, Quality, Assembly
2915 days ago
- SRBreak is a read-depth and split-read package written in R for identifying copy-number variants in next-generation sequencing datasets. Note: SBReak was designed to work for multiple samples. It can work for >= 2 samples, but we suggest that users should use >= 5 samples as in the work ...
Tags: SRBreak, Read-Depth, Split-Read, Framework, Breakpoints, Copy-Number, Variable, Regions
2166 days ago
Mobyle: a new full web bioinformatics framework
Mobyle, to provide a flexible and usable Web environment for defining and running bioinformatics analyses. It embeds simple yet powerful data management features that allow the user to reproduce analyses and to combine tools using a hierarchical typing system. Mobyle offers invocation of services...Tags: Mobyle, full, web, bioinformatics, framework
2293 days ago
Frontend: Perl Web framework documentation - Andrej Sali Lab
The frontend is a set of Perl classes that displays the web interface, allowing a user to upload their input files, start a job, display a list of all jobs in the system, and get back job results. The main saliwebfrontend class must be subclassed for each web service. This class is then...Tags: Frontend, Perl, Web, framework, documentation, Andrej Sali, Lab
2292 days ago
mojolicious: a next generation web framework for the Perl programming language.
Back in the early days of the web, many people learned Perl because of a wonderful Perl library called CGI. It was simple enough to get started without knowing much about the language and powerful enough to keep you going, learning by doing was much fun. While most of the techniques used are...Tags: mojolicious, next generation, web, framework, Perl, programming, language
2288 days ago
repeat-aware: Repeat aware scaffolding evaluation framework by Igor Mandric
Genome scaffolding is a classical challenging problem in bioinformatics. It refers to joining assembly contigs into chains (called scaffolds). The join between two contigs A and B is considered correct if: Their relative orientation is correct Their relative order is correct The gap estimate...Tags: Repeat, aware, scaffolding, evaluation, framework, Igor, Mandric, repeat-aware
2220 days ago
nQuire: a statistical framework for ploidy estimation using next generation sequencing
nQuire provides a statistical framework to study organisms with intraspecific variation in ploidy. nQuire is likely to be useful in epidemiological studies of pathogens, artificial selection experiments, and for historical or ancient samples where intact nuclei are not preserved. It is implemente...Tags: nQuire, statistical, framework, ploidy, estimation, next, generation, sequencing, NGS
2024 days ago
PilonGrid: parallel wrapper around the Pilon framework
The distribution is a parallel wrapper around the Pilon framework The pipeline is composed of bash scripts, an example mapping.fofn which shows how to input your fastq files (you give paths to the R1 file), and how to launch the pipeline.Tags: PilonGrid, parallel, wrapper, Pilon, framework
1953 days ago
Biotite: A general framework for computational biology
The package is open source and freely available at GitHub (https://github.com/biotite-dev/biotite). This package is simple to use especially for the beginners in programming and computationally efficient because of the implementation of Numpy and Cython. Biotite consists of four sub packages...Tags: Biotite, general, framework, computational, biology
1949 days ago
nQuire: A statistical framework for ploidy estimation using NGS short-read data
nQuire implements a set of commands to estimate ploidy level of individuals from species, where recent polyploidization occurred and intraspecific ploidy variation is observed. Specifically, nQuire uses next-generation sequencing data to distinguish between diploids, triploids and tetraploids, on...Tags: statistical, framework, ploidy, estimation, NGS, short-read, data
1905 days ago
