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iggdb

Database of genomes integrated from the gut microbiome and other environments

jd-assistant

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kieft_and_zhou_et_al._2020

lao_multiomics_crispr_imges

magpurify

Improvement of metagenome-assembled genomes

main_paper_figures

Code used to generate figures for the MetaSUB Main Paper Released August 2019

metachip

Horizontal gene transfer (HGT) identification pipeline

metagenomicantibioticresistance

NastyBugs: a simple method for extracting antimicrobial resistance information from metagenomes

metagenomics2021

Metagenomics course

metagenomic_resistome

This repository contains all the scripts used for metagenomic processing and resistome. First, metagenome sequences from cattle feces were analyzed with AmrPlusPlus for sequence processing and ARG annotations with the MEGARES 2.0 database. Then, host-removed metagenomes were used for DNA assembly and further annotations with DeepARG, CARD, and HMD-ARG which are protein databases to identify antimicrobial determinants. Finally, ARG-host identification was carried out by identifying taxa associated with ARG-carrying contigs and co-occurrence networks between bacterial taxa and ARGs. Statistical analyses were used to identify assembler performance and resistome composition.

metawibele

MetaWIBELE: Workflow to Identify novel Bioactive Elements in microbiome

metawrap

MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis

mgefinder

A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.

mobilegeneticelementdatabase

Contains a fasta format database of a large variety of mobile genetic elements and an annotation file

multi-metagenome

Scripts and tutorials on how to assemble individual microbial genomes from metagenomes

nf-anvio-pangenome

Analyze a set of genomes with the anvi'o pangenome pipeline

note

pb-metagenomics-tools

pb-metagenomics-tools

plascad

Plascad is a computationally efficient tool designed for plasmids classification, antibiotic resistance genes (ARGs) annotation and plasmid visualization.

pool-reference

prokka_tag_args_with--proteins

Procedure to annotate antibiotic resistance genes (ARGs) referenced by the CARD database using PROKKA

refinem

A toolbox for improving metagenome-assembled genomes.

selected-file-copy

Copies a list of files from one folder to another

snipe

Highly sensitive pathogen detection

split-folder

Split a big folder into several.

sunbeam

A robust, extensible metagenomics pipeline

table2itol

Generating iToL annotations from Spreadsheet or CSV files

tiger

Target / Integrative Genetic Element Retriever: precisely maps IGEs (a defined type of genomic island) in bacterial and archaeal genomes; package also includes orthogonal program Islander

track_structural_variants

A set of scripts used for tracking structural variations around a gene of interest

ublastx_stageone

This is the source code for multisamples ARGs profiling using SARG2.0 database