shangshanzhizhe

deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

popgen-notes

Population genetics notes

DESeq2

Differential expression of RNA-seq data using the Negative Binomial

pyfastx

a python package for fast random access to sequences from plain and gzipped FASTA/Q files

pangene

Constructing a pangenome gene graph

f5c

Ultra-fast methylation calling and event alignment tool for nanopore sequencing data (supports CUDA acceleration)

PanDepth

An ultra-fast and efficient genomic tool for coverage calculation

cLoops

Accurate and flexible loops calling tool for 3D genomic data.

perfect-bioinformatic-tools

What should perfect bioinformatic tools be like?

score

Tools to work with GWAS-VCF summary statistics files

minipileup

Simple pileup-based variant caller

SNPhylo

A pipeline to generate a phylogenetic tree from huge SNP data

panpop

Application of pan-genome for population

twisst

Topology weighting by iterative sampling of sub-trees

QuIBL

Quantifying Introgression via Branch Lengths

GONE

GONE: Scripts, programs and an example data set

biser

A fast tool for detecting and decomposing segmental duplications in genome assemblies

NgsRelate

Broccoli

orthology assignment using phylogenetic and network analyses

ngsLD

Calculation of pairwise Linkage Disequilibrium (LD) under a probabilistic framework

SVarp

Phased structural variant discovery in pangenomes

genotyphi

Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)

pantera

Identification of transposable element families from pangenome polymorphisms

graphphylo

visualization of phylogenetic output files

GScour

Genome-wide detection of positive selection

HiCube

A lightweight web application for interactive visualization of multiscale and multimodal Hi-C and 3D genome data

sam2psl

Convert SAM format to PSL format

sanger.dk

Tribute to https://sanger.dk but as a gif since flash is over... (https://developer.mozilla.org/en-US/docs/Plugins/Flash_Activation:_Browser_Comparison)

cuteFC

Regenotyping structural variants through an accurate and efficient force-calling method

kitchenflies