SPAdes Genome Assembler

Software for prediction of plasmid sequences in metagenomic assemblies

Metagenomic binning based on Hi-C data

Deep learning for Metagenome Assembly Error Detection

Binnacle: Using Scaffolds to Improve the Contiguity and Quality of Metagenomic Bins

Identifying misassemblies via deep learning

Environmental metagenomics, Spring 2021, Physalia Courses

Workflow for metagenome assembly

Create a blobplot of a holobiont assembly without a reference genome. Example code and data are provided.

MetaBolt: Lightning fast & automated metagenomic pipeline powered by Nextflow

Statistical package for metaome denovo assembly results.

Code associated with the Ley Lab animal gut metagenome assembly project

This project aims do describe and explore the metagenomes of fern species of the genus Azolla.

PostgreSQL analytics warehouse integrating de novo viral metagenome assembly, CheckV quality control, and geNomad taxonomic/functional annotations to profile condition-associated bacteriophage populations in an ASD vs. TD fecal microbiota transplant gnotobiotic mouse model (Sharon et al. 2019).

Run multiple metagenome filtering programs using Docker containers

Description of the bioinformatic workflow applied in Passaro et al 2019

Graph-based metagenomic binning and context-aware scaffolding workflow for improving microbial genome reconstruction from short-read assemblies.