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anuraghazra.github.io

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baldur

Variant (SNV and small indel) calling from ONT sequencing data on the mitochondria

bioinfokit

Bioinformatics data analysis and visualization toolkit

clair3

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

combisv

Combine structural variation outputs from long sequencing reads into a superior call set

consplice

Constrained Splicing python module

csama2016

Repository for CSAMA 2016 course material

csvtk

A cross-platform, efficient and practical CSV/TSV toolkit in Golang

cutesv

Long read based human genomic structural variation detection with cuteSV

cyvcf2

cython + htslib == fast VCF and BCF processing

datasharing

The Leek group guide to data sharing

denovo_sv_validation

Pipeline for validation of de novo SVs

dna-seq-analysis

DNA sequencing analysis notes from Ming Tang

dnsv

A tool for de novo variation detection from structural variations

duet

SNP-Assisted SV Calling and Phasing Using ONT

ensembl-vep

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants

expansionhunterdenovo

A suite of tools for detecting expansions of short tandem repeats

fastcat

Simple utility to concatenate .fastq(.gz) files whilst creating a summary of the sequences.

flye

De novo assembler for single molecule sequencing reads using repeat graphs

funncion

predicting LOF vs GOF variant effects in SCN and CACNA1 genes

genomicsnotebook

Jupyter Notebooks on Azure for Genomics Data Analysis

ggsashimi

Command-line tool for the visualization of splicing events across multiple samples

gwasglue

Linking GWAS data to analytical tools in R

hap.py

Haplotype VCF comparison tools

hdl

High-definition likelihood inference of genetic correlations (HDL)

home

DMR Identification Tool

irfinder

ldsc

LD Score Regression (LDSC)

longphase

me-class2

Integrative analysis of DNA methylation and expression data. Can integrate 5mC and/or 5hmC data.