balabanmetin

cromwell

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

CNRein

Single-Cell Copy Number Calling with Evolution-Aware Deep Reinforcement Learning

transformers

🤗 Transformers: State-of-the-art Machine Learning for Pytorch, TensorFlow, and JAX.

cyvcf2

cython + htslib == fast VCF and BCF processing

GooglePhotosTakeoutHelper

Script that organizes the Google Takeout archive into one big chronological folder

rclone

"rsync for cloud storage" - Google Drive, S3, Dropbox, Backblaze B2, One Drive, Swift, Hubic, Wasabi, Google Cloud Storage, Azure Blob, Azure Files, Yandex Files

wol

Reference Phylogeny for Bacterial and Archaeal Genomes

TurboMac

Stops CPU throttling on Intel-based Macs

rust-mdbg

minimizer-space de Bruijn graphs (mdBG) for whole genome assembly

ASTER

Accurate Species Tree EstimatoR series: a family of optimation algorithms for species tree inference implemented in C++ (including ASTRAL-Pro & Weighted ASTRAL)

Hardware

The devices I have, what runs on them, their configurations, issues, solutions, and associated projects

spp_dcj

pipeline

[Archived] SnakeMake pipeline to run BlobTools on public assemblies

ratarmount

Access large archives as a filesystem efficiently, e.g., TAR, RAR, ZIP, GZ, BZ2, XZ, ZSTD archives

kmeans1d

A Python package for optimal 1D k-means clustering.

PPLACER

DEPP

CONSULT

Accurate contamination removal using locality-sensitive hashing

PEWO

Phylogenetic Placement Evaluation Workflows : Benchmark placement software and different reference trees

phylosim

An R package for the Monte Carlo simulation of sequence evolution

lbzip2

Parallel bzip2 utility

zstd

Zstandard - Fast real-time compression algorithm

trimal

A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0

newick-tools

Visualize and perform a multitude of operations on newick files

TreeCluster

Efficient phylogenetic clustering of viral sequences

INSTRAL

Discordance-aware Phylogenetic Placement using Quartet Scores

fastDNA

CMash

Fast and accurate set similarity estimation via containment min hash

MinHashMetagenomics

Fast approximation of similarity for sets of very different sizes

CHM13

The complete sequence of a human genome