omicsnut

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New York Genome Center

New York, USA

https://about.me/omicsnut

Rajeeva Lochan Musunuri's starred repositories

QuickEd

QuickEd is a high-performance exact sequence alignment based on the bound-and-align paradigm.

Language:C++MIT2100

Lancet2

v2.x of the microassembly based somatic variant caller

Language:C++BSD-3-Clause1400

cpp-mdbg

C++ implementation of the minimizer space De Bruijn graph assembler.

Language:C++300

ropebwt3

BWT construction and search

Language:CNOASSERTION8900

nvitop

An interactive NVIDIA-GPU process viewer and beyond, the one-stop solution for GPU process management.

Language:PythonApache-2.0467900

MMseqs2

MMseqs2: ultra fast and sensitive search and clustering suite

Language:CGPL-3.0136900

openbb-agents

R&D playground to play with agents and OpenBB

Language:Python40700

biowasm

WebAssembly modules for genomics

Language:HTMLMIT21500

stumpy

STUMPY is a powerful and scalable Python library for modern time series analysis

Language:PythonNOASSERTION363400

gam-changer

Editing machine learning models to reflect human knowledge and values

Language:JavaScriptMIT12100

ebm2onnx

A tool to convert EBM models to ONNX

Language:PythonMIT2000

sam2

The repository provides code for running inference with the Meta Segment Anything Model 2 (SAM 2), links for downloading the trained model checkpoints, and example notebooks that show how to use the model.

Language:Jupyter NotebookApache-2.01124900

alfred

BAM Statistics, Feature Counting and Annotation

Language:C++BSD-3-Clause14300

wally

Wally: Visualization of aligned sequencing reads and contigs

Language:C++BSD-3-Clause10600

uv

An extremely fast Python package and project manager, written in Rust.

Language:RustApache-2.02170900

strobealign

Aligns short reads using dynamic seed size with strobemers

Language:C++MIT14200

minisv

Lightweight mosaic/somatic SV caller for long reads (WIP)

Language:JavaScriptMIT2700

cs-video-courses

List of Computer Science courses with video lectures.

Rust

All Algorithms implemented in Rust

Language:RustMIT2220500

ClickHouse

ClickHouse® is a real-time analytics DBMS

Language:C++Apache-2.03694100

Best-websites-a-programmer-should-visit

:link: Some useful websites for programmers.

MIT6125600

GraffiTE

GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.

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vg_wdl

Workflow Description Language (WDL) scripts for common vg workflows

Language:WDLMIT1600

vip

Variant Interpretation Pipeline

Language:ShellLGPL-3.02300

mumemto

Multi-MUM and MEM finding across collections of sequences

Language:C++GPL-3.0500

figeno

Tool for plotting sequencing data along genomic coordinates.

Language:PythonGPL-3.024600

vcfpp

a C++ API of htslib to be easily integrated and safely used. More importantly, it can be callled seamlessly in R/Python/Julia etc.

Language:C++MIT2300

python-fire

Python Fire is a library for automatically generating command line interfaces (CLIs) from absolutely any Python object.

Language:PythonNOASSERTION2693300

fastq-dl

Download FASTQ files from SRA or ENA repositories.

Language:PythonMIT27100

redis-roaring

Roaring Bitmaps for Redis

Language:CMIT34500