cerebis

LKH3

Github mirror of Keld Helsgaun's wonderful LKH3 project.

bin3C

Extract metagenome-assembled genomes (MAGs) from metagenomic data using Hi-C.

sim3C

Read-pair simulation of 3C-based sequencing methodologies (HiC, Meta3C, DNase-HiC)

qc3C

Reference-free quality assessment for Hi-C sequencing data

meta-sweeper

Parametric sweep of simulated microbial communities and metagenomic sequencing.

bcubed

bcubed and weighted bcubed external validation index

CAT

CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)

Deepbinner

a signal-level demultiplexer for Oxford Nanopore reads

DeepVirFinder

Identifying viruses from metagenomic data by deep learning

DRAM

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

genomics_notes

A collection of scripts and notes related to genomics and bioinformatics

gfa_io

A simple module for reading GFA v1 files.

gi2020_poster

Genome Informatics 2020 Poster

GraphBin2

GraphBin2: Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs

GraphPlas

GraphPlas: Assembly Graph Assisted Recovery of Plasmidic Contigs from TGS Assemblies

HiCzin

HiCzin: Normalizing metagenomic Hi-C data and detecting spurious contacts using zero-inflated negative binomial regression

i3seqdb

Tracking and workflow instrumentation for NGS

MARVEL

MARVEL: Metagenomic Analyses and Retrieval of Viral ELements

maw

MAW: a suite on the computation and application of Minimal Absent Words

MultiQC

Aggregate results from bioinformatics analyses across many samples into a single report.

MultiQC_TestData

Test data for MultiQC. See https://github.com/ewels/MultiQC

nucleotide-transformer

🧬 Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics

Nullomers-Assessor

Nullomers Assessor: A computational method for statistical evaluation of nullomers & minimal absent words

Outbreak_EnrichmentCulture

PlasClass

A tool to classify sequences of plasmid or chromosomal origin. A paper describing this tool is available at: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007781

proxigenomics_toolkit

A collection of classes and methods for the analysis of 3C-based sequencing data.

pygraphistry

PyGraphistry is a Python library to quickly load, shape, embed, and explore big graphs with the GPU-accelerated Graphistry visual graph analyzer

TMbed

Transmembrane proteins predicted through Language Model embeddings

vHULK

viral Host UnveiLing Kit (vHULK)

ViralCC

ViralCC: leveraging metagenomic proximity-ligation to retrieve complete viral genomes