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gnnome

A framework for training graph neural networks to untangle assembly graphs obtained from OLC-based de novo genome assemblers.

gnns-hamiltonian-cycles

Supplementary code for "Finding Hamiltonian cycles with graph neural networks"

graphmap2

GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1

heron-raven

Development of Raven - Heron branch

herro

HERRO is a highly-accurate, haplotype-aware, deep-learning tool for error correction of Nanopore R10.4.1 or R9.4.1 reads (read length of >= 10 kbps is recommended).

hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

i002c

Telomere-to-Telomere diploid Indian Genome

merlion

metagenomicsbenchmark

neurallayout

A GNN model that executes simplification algorithms used in the layout phase of de novo genome assembly process.

ra

Assembler for raw de novo genome assembly of long uncorrected reads.

racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads

ram

ratlesnake

raven

De novo genome assembler for long uncorrected reads

rinalmo

RiboNucleic Acid (RNA) Language Model

rnaseqeval

A tool for evaluating RNA seq mapping

rockfish

rockfish-old

Deep learning based method for detecting DNA base modifications

roko

A deep learning consensus polisher

scara

SCARA - scaffolding with long reads

t2t-assemblies

T2T assemblies of human and durian genomes

tarantula