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alphathal

Pipeline for retrieving reads from the Alpha Thalassemia region

bam2mpg

Software for calling variants from next-generation sequence data.

bardcnv

BardCNV calls copy number variants from next generation sequencing data.

bioconda-recipes

Conda recipes for the bioconda channel.

github_issues

Python software to create and retrieve GitHub issues and write spreadsheets to Google Sheets with issue metadata

issue-dump

Place to send issues created in error

issue-playground

Testing repository for issue templates and trigger to google sheet

latestageeecs

Statistical analysis software used in Rudd et al., "KLF3 and PAX6 are candidate driver genes in late-stage, MSI-hypermutated endometrioid 2 endometrial carcinomas"

mlgenofeatures

mlgenotype

Python package for training and using machine learning models to recognize structural variants using features of aligned short read data

mmbvariantcalling

Scripts and updates for running the variant pipeline described in "Variant Calling From Next Generation Sequence Data" by Nancy F. Hansen

nhansen

nhansen.github.io

Documentation for Nancy Hansen's software tools

nhgri-bw2

Software to automate tasks for performing biowulf2 analyses remotely from a different server.

novograph

NovoGraph: building whole genome graphs from long-read-based de novo assemblies

q100bench

Software for comparing genome assemblies and read datasets to a benchmark genome like the Q100 project's HG002v1.0.1

rfgenotypemanuscript2023

Scripts and data files for "Random forest classifiers trained on simulated data enable accurate short read-based genotyping of structural variants in the alpha thalassemia genomic region"

shimmer

Shimmer is a software package for the characterization of genetic differences between two very similar samples, e.g., a tumor sample and its matched normal tissue sample.

sleepinbredpanel

svanalyzer

Tools for the analysis of structural variation in genomes

t2tvariants

Code used for Aganezov et al., A complete reference genome improves analysis of human genetic variation. bioRxiv, 2021.