LeeBergstrand

grok-1

Grok open release

llm.c

LLM training in simple, raw C/CUDA

devika

Devika is an Agentic AI Software Engineer that can understand high-level human instructions, break them down into steps, research relevant information, and write code to achieve the given objective. Devika aims to be a competitive open-source alternative to Devin by Cognition AI.

FreeAskInternet

FreeAskInternet is a completely free, PRIVATE and LOCALLY running search aggregator & answer generate using MULTI LLMs, without GPU needed. The user can ask a question and the system will make a multi engine search and combine the search result to LLM and generate the answer based on search results. It's all FREE to use.

PowerInfer

High-speed Large Language Model Serving on PCs with Consumer-grade GPUs

gpt-investor

seqkit

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

hail

Cloud-native genomic dataframes and batch computing

attention_sinks

Extend existing LLMs way beyond the original training length with constant memory usage, without retraining

bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

Porechop

adapter trimmer for Oxford Nanopore reads

rgi

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.

InfLLM

The code of our paper "InfLLM: Unveiling the Intrinsic Capacity of LLMs for Understanding Extremely Long Sequences with Training-Free Memory"

NextPolish

Fast and accurately polish the genome generated by long reads.

sunbeam

A robust, extensible metagenomics pipeline

sylph

ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.

singlem

Novelty-inclusive microbial community profiling of shotgun metagenomes

mob-suite

MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies

abPOA

abPOA: an SIMD-based C library for fast partial order alignment using adaptive band

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.

hybracter

Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.

pyMSAviz

MSA(Multiple Sequence Alignment) visualization python package for sequence analysis

woltka

Woltka: a versatile meta'omic data classifier

gtdb_to_taxdump

Convert GTDB taxonomy to NCBI taxdump format

CompareM2

🦠📇 Microbial genomes-to-report pipeline

mobilome-annotation-pipeline

noveltree

NovelTree is a highly parallelized and computationally efficient phylogenomic workflow that infers gene families, gene family trees, species trees, and gene family evolutionary history.

psm3mkv

psm3mkv: A package to evaluate the fit and efficiency of three state oncology cost-effectiveness model structures

rotary

Assembly/annotation workflow for Nanopore-based microbial genome data containing circular DNA elements

seguid-python

SEGUID v2: Checksums for Linear, Circular, Single- and Double-Stranded Biological Sequences