pepper
PEPPER-Margin-DeepVariant (by kishwarshafin)
edgecase
A framework for extracting telomeric reads from single-molecule sequencing experiments, describing their sequence variation and motifs, and for haplotype inference. (by LankyCyril)
| pepper | edgecase | |
|---|---|---|
| 1 | 1 | |
| 231 | 14 | |
| - | - | |
| 0.0 | 2.1 | |
| 4 months ago | 4 months ago | |
| Python | Python | |
| MIT License | GNU General Public License v3.0 only |
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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.
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edgecase
Posts with mentions or reviews of edgecase.
We have used some of these posts to build our list of alternatives
and similar projects.
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Know a tool that visualizes read sequence extending beyond reference coordinates?
that said, just looking at the raw "show softclipped sequence" in e.g. igv may not be the best scenario either, so creating a custom visualization may be needed anyways. here is another tool i found https://github.com/lankycyril/edgecase from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8256856/
What are some alternatives?
When comparing pepper and edgecase you can also consider the following projects:
Clairvoyante - Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing
ariba - Antimicrobial Resistance Identification By Assembly
pipeline-structural-variation - Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
pysradb - Package for fetching metadata and downloading data from SRA/ENA/GEO