eskutkaan

Big-BWT

modified from gitlab.com/manzai/Big-BWT to support fasta files

gffcompare

classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF

straglr

Tandem repeat expansion detection or genotyping from long-read alignments

pytorch

Tensors and Dynamic neural networks in Python with strong GPU acceleration

methylartist

Tools for plotting methylation data in various ways

savana

Somatic structural variant caller for long-read data

racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:

PureCN

Copy number calling and variant classification using targeted short read sequencing

epa-ng

Massively parallel phylogenetic placement of genetic sequences

HapHiC

HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data

quickmerge

A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.

vcf2phylip

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

PDF-Extract-Kit

A Comprehensive Toolkit for High-Quality PDF Content Extraction

facets2n

Algorithm to implement Fraction and Allelic Copy number Estimate from Tumor/normal Sequencing using unmatched normal sample(s) for log ratio calculations

HiTE

High-precision TE Annotator

ModDotPlot

parallel-hashmap

A family of header-only, very fast and memory-friendly hashmap and btree containers.

ChIPseeker

:dart: ChIP peak Annotation, Comparison and Visualization

DirectHRD

T2T-Polish

Evaluation and polishing workflows for T2T genome assemblies

positron

Positron, a next-generation data science IDE

ruby

The Ruby Programming Language

C

Collection of various algorithms in mathematics, machine learning, computer science, physics, etc implemented in C for educational purposes.

obs-studio

OBS Studio - Free and open source software for live streaming and screen recording

neovim

Vim-fork focused on extensibility and usability

openst

Open-ST: profile and analyze tissue transcriptomes in 3D with high resolution in your lab

CLI11

CLI11 is a command line parser for C++11 and beyond that provides a rich feature set with a simple and intuitive interface.

linux

Linux kernel source tree

pla-index

sapling

SAPLING: Suffix Array Piecewise Linear INdex for Genomics