pepper
PEPPER-Margin-DeepVariant (by kishwarshafin)
pipeline-structural-variation
Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data (by nanoporetech)
| pepper | pipeline-structural-variation | |
|---|---|---|
| 1 | 1 | |
| 231 | 87 | |
| - | - | |
| 0.0 | 1.6 | |
| 4 months ago | over 2 years ago | |
| Python | Python | |
| MIT License | GNU General Public License v3.0 or later |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
pepper
Posts with mentions or reviews of pepper.
We have used some of these posts to build our list of alternatives
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pipeline-structural-variation
Posts with mentions or reviews of pipeline-structural-variation.
We have used some of these posts to build our list of alternatives
and similar projects.
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Help with Nanopore sequencing information and resources for gross chromosomal rearrangement analysis
Regarding analysis, I would suggest reading papers that use nanopore sequencing to identify structural variants and to read their method section. This can be on any species really, the approach is the same between them. A standard workflow can be found on ONT's github and on their EPI2ME labs platform (the github one is the most recent and up-to-date).
What are some alternatives?
When comparing pepper and pipeline-structural-variation you can also consider the following projects:
Clairvoyante - Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing
bonito - A PyTorch Basecaller for Oxford Nanopore Reads
Pipeliner - An open-source and scalable solution to NGS analysis powered by the NIH's Biowulf cluster.
Sniffles - Structural variation caller using third generation sequencing
edgecase - A framework for extracting telomeric reads from single-molecule sequencing experiments, describing their sequence variation and motifs, and for haplotype inference.