malonge

microservices-demo

Sample cloud-first application with 10 microservices showcasing Kubernetes, Istio, and gRPC.

mummer

Mummer alignment tool

yggdrasil

A framework for connecting scientific models across languages and scales.

compleasm

A genome completeness evaluation tool based on miniprot

FisherExact

Fisher exact test for mxn contingency table in python

ModDotPlot

statsmodels

Statsmodels: statistical modeling and econometrics in Python

stmol

This is the repository for the Stmol project, a Streamlit component that uses py3Dmol to render molecules.

miniprot

Align proteins to genomes with splicing and frameshift

python-barcode

㊙️ Create standard barcodes with Python. No external dependencies. 100% Organic Python.

wfmash

base-accurate DNA sequence alignments using WFA and mashmap2

WFA-paper

Wavefront alignment algorithm (WFA): Fast and exact gap-affine pairwise alignment

WFA2-lib

WFA-lib: Wavefront alignment algorithm library v2

BiWFA-paper

Bidirectional WFA (Paper)

miniwfa

A reimplementation of the WaveFront Alignment algorithm at low memory

scikit-learn

scikit-learn: machine learning in Python

agc

Assembled Genomes Compressor

manim

Animation engine for explanatory math videos

LJA

bioframe

Genomic Interval Operations on Pandas DataFrames

pepper

PEPPER-Margin-DeepVariant

d3

Bring data to life with SVG, Canvas and HTML. :bar_chart::chart_with_upwards_trend::tada:

kmcp

Accurate metagenomic profiling && Fast large-scale sequence/genome searching

plotsr

Tool to plot synteny and structural rearrangements between genomes

verkko

snap

Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data

cuteSV

Long read based human genomic structural variation detection with cuteSV

svim

Structural Variant Identification Method using Long Reads

pin_hic

A Hi-C scaffolding method

bonito

A PyTorch Basecaller for Oxford Nanopore Reads