A Python pipeline for ACMG‑like variant classification from ANNOVAR/SnpEff outputs, generating tables and styled PDF reports with allele frequencies, variant categories, top genes, and detailed pat…

Next generation sequencing reads de novo assembler.

The second version of the Kraken taxonomic sequence classification system

aweMAGs: a fully automated workflow for eukariotic MAGs

Pilon is an automated genome assembly improvement and variant detection tool

Reference-free profiling of polyploid genomes

Genome-scale protein function classification

MetaDome is aimed at professionals in the (bio-)medical field of human genetics who wish to visualize the position of their mutation of interest in the context of general population-based genetic …

ggplot2: elegant graphics for data analysis

my Vim/Tmux config 💪⚡

A curated list of paid and unpaid open-source opportunities, projects, and resources for bioinformatics beginners to gain experience, build portfolios and grow in the field

Comprehensive benchmark of structural variant callers

Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools

The Missing Semester of Your CS Education 📚

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

A quality control analysis tool for high throughput sequencing data

Flake8 plugin for Vim

"Slides" and supplemental info from my August 3rd 2016 NYC Vim talk

Pangolin is a deep-learning method for predicting splice site strengths.

A deep learning-based tool to identify splice variants

Machine Learning Course, Sharif University of Technology

Mondo Disease Ontology

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

Code to run analysis in "A Multiplexed Assay for Exon Recognition Reveals that an Unappreciated Fraction of Rare Genetic Variants Cause Large-Effect Splicing Disruptions"

CADD scripts release for offline scoring. For more information about CADD, please visit our website

This repo contains scripts for tutorials on my YouTube channel (youtube.com/@elmium)