Alienomics
Automated pipeline for HGT and contaminant detection in an assembled, annotated genome
| Project Name | Stars | Downloads | Repos Using This | Packages Using This | Most Recent Commit | Total Releases | Latest Release | Open Issues | License | Language |
|---|---|---|---|---|---|---|---|---|---|---|
| Deepvariant | 2,978 | 5 months ago | 8 | bsd-3-clause | Python | |||||
| DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. | ||||||||||
| Gatk | 1,576 | 2 | 2 months ago | 46 | March 16, 2023 | 1,299 | other | Java | ||
| Official code repository for GATK versions 4 and up | ||||||||||
| Snakepipes | 359 | 3 months ago | 34 | mit | Python | |||||
| Customizable workflows based on snakemake and python for the analysis of NGS data | ||||||||||
| Ngsplot | 231 | a year ago | 55 | other | R | |||||
| Quick mining and visualization of NGS data by integrating genomic databases | ||||||||||
| Ngb | 151 | 3 months ago | 290 | mit | Java | |||||
| New Genome Browser (NGB) - a Web - based NGS data viewer with unique Structural Variations (SVs) visualization capabilities, high performance, scalability, and cloud data support | ||||||||||
| Viral Ngs | 129 | 4 years ago | 60 | other | Python | |||||
| Viral genomics analysis pipelines | ||||||||||
| V Pipe | 119 | 4 months ago | 27 | apache-2.0 | Jupyter Notebook | |||||
| V-pipe is a pipeline designed for analysing NGS data of short viral genomes | ||||||||||
| Tadbit | 89 | a year ago | 58 | gpl-3.0 | Python | |||||
| TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models | ||||||||||
| Mcclintock | 83 | 4 months ago | 6 | Python | ||||||
| Meta-pipeline to identify transposable element insertions using next generation sequencing data | ||||||||||
| Ngseasy | 76 | 7 years ago | 9 | gpl-2.0 | Shell | |||||
| Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation) | ||||||||||
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