This repo includes ChatGPT prompt curation to use ChatGPT better.

non-redundant, compressed, journalled, file-based storage for biological sequences

Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image

igv.js standalone page generator and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"

VarDict Java port

A curated collection of Nextflow implementation patterns

A set of data tools in Python

Low-code framework for building custom LLMs, neural networks, and other AI models

Aligns short reads using dynamic seed size with strobemers

Microsatellite instability (MSI) detection for cfDNA samples.

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

A curated list of nextflow based pipelines

Nextflow training material for introductory tutorial

Tools for handling Unique Molecular Identifiers in NGS data sets

Reliable CNV detection in targeted sequencing applications

Assign gene names to regions in a BED file

Comprehensive benchmark of structural variant callers

GRIDSS: the Genomic Rearrangement IDentification Software Suite

ExomeDepth R package for the detection of copy number variants in exomes and gene panels using high throughput DNA sequencing data.

Copy Number Variation Detection In Next-generation sequencing Gene panels was designed for small (single-exon) copy number variation (CNV) detection in high coverage next-generation sequencing (NGS…

Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data

CNV detection tool for targeted NGS panel data

Framework to benchmark algorithms when detecting germline copy number variations (CNVs) from NGS data

notes about machine learning

Copy number variant detection from targeted DNA sequencing

Plumb a PDF for detailed information about each char, rectangle, line, et cetera — and easily extract text and tables.

A Python library for reading and writing PDF, powered by QPDF

All-FIT - Allele-Frequency-based Imputation of Tumor Purity

Frontend for Genome Nexus 🎉