/tools

tools

A collection of tools that are useful, and a list of tools that might be useful and warrant further investigation/use

Brentp heads the list:

Visualisation
Samplot rapid, multi-sample structural variant visualization
IPYIGV Python library for embedding IGV tracks
Graph Gallery A collection of plots made with python - using MatplotLib, Seaborn and Plotly
IGV Reports untested, need to look into

Mutational Signature tools
Cosmic Signatures
Signature Tools From Serena Nik.Zainals group

Curation
Ella open source curation tool, out of Oslo
Scout open source curation tool, ESR are using it

Testing
Tox Automation testing?
Test driven Development Just something to keep in mind.

Pipeline tools

Workflow Mangement
CWL
Snakemake
Arvados
[Panoptes] Snakemake workflow monitor
[Mariner]{https://github.com/uc-cdis/mariner) Gen3 Workflow execution service
Terra

Variant Calling
Snps and Indels
Varlociraptor untested

Annotation
VCFAnno
Cancer Genome Interpreter
MyVariant python library to query/retrieve variant data
ellaAnno annotation tool to feed into Ella
g2p-aggregator VICC annotation collator

Filtering
silvar filtering and rapid query of individuals, trios and groups
somalier filtering and extraction of informative sites

VCF manipulation
VCFtools
pyVCF Python tools for vcf access

Coverage
Seqcover
[Mosdepth](https://github.com/brentp/mosdepth]
goleft more brentp magic

Conversion tools
Gene Number Conversion

Precision Medicine Infrastructure
htsget
Passports/Visas Protocol specification only, not implemented
Beacons
Data Repository Service

Reproducibility
Truwl New tool, needs community take up

Python Tools
Poetry Dependency management
mypy Static type checking