edgecase
ariba
edgecase | ariba | |
---|---|---|
1 | 1 | |
14 | 154 | |
- | 1.9% | |
2.1 | 3.0 | |
4 months ago | 7 months ago | |
Python | Python | |
GNU General Public License v3.0 only | GNU General Public License v3.0 or later |
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edgecase
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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/
ariba
What are some alternatives?
pipeline-structural-variation - Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
abricate - :mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes
pysradb - Package for fetching metadata and downloading data from SRA/ENA/GEO
galaxy - Data intensive science for everyone.
MGEfinder - A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
abritamr - A pipeline for running AMRfinderPlus and collating results into functional classes
16SMaRT - 16s rRNA Sequencing Meta-analysis Reproducibility Tool (using mothur).
hgvs - Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
deepvariant - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.