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Search results for python metagenomics

123 search results found

An analysis and visualization platform for 'omics data

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

ATLAS - Three commands to start analyzing your metagenome data

Metaphlan ⭐ 242

MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

Rapid comparison and dereplication of genomes

Insilicoseq ⭐ 158

🚀 A sequencing simulator

Metagem ⭐ 155

💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

Camisim ⭐ 115

CAMISIM: Simulating metagenomes and microbial communities

Rapdtool ⭐ 110

Rapid Profiling and Deconvolution Tool for Metagenomes

SemiBin: metagenomics binning with self-supervised deep learning

Recentrifuge ⭐ 83

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

Graphbin ⭐ 80

✨🧬 Refined binning of metagenomic contigs using assembly graphs

ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more

Metagenomics Index Correction ⭐ 67

A package for designing compact and comprehensive capture probe sets.

A hybrid assembly and MAG recovery pipeline (and more!)

Deepmicrobes ⭐ 61

DeepMicrobes: taxonomic classification for metagenomics with deep learning

Woltka: a versatile meta'omic data classifier

🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes

Predict AMPs in (meta)genomes and peptides

A general metagenomics data mining system focus on robust microbiome research

GEne Cluster prediction with COnditional random fields.

Grabseqs ⭐ 44

A utility for easy downloading of reads from next-gen sequencing repositories like NCBI SRA

Metachip ⭐ 42

Horizontal gene transfer (HGT) identification pipeline

Keggcharter ⭐ 40

A tool for representing genomic potential and transcriptomic expression into KEGG pathways

Bhattlab_workflows ⭐ 39

Computational workflows for metagenomics tasks, by the Bhatt lab

Metacoag ⭐ 36

🚦🧬 Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs

Autometa ⭐ 35

Autometa: Automated Extraction of Genomes from Shotgun Metagenomes

Graph-based assembly phasing

Kraken Biom ⭐ 33

Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).

Covid 19 Signal ⭐ 32

Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.

Meta-Omics Software for Community Analysis

Charcoal ⭐ 31

Remove contaminated contigs from genomes using k-mers and taxonomies.

Prophyle ⭐ 30

Accurate, resource-frugal and deterministic DNA sequence classifier.

Strainscan ⭐ 30

High-resolution strain-level microbiome composition analysis tool based on reference genomes and k-mers

Wochenende ⭐ 30

Deprecated see https://github.com/MHH-RCUG/nf_wochenende : A whole Genome/Metagenome Sequencing Alignment Pipeline in Python3

HMM-based identification and categorization of iron genes and iron gene operons in genomes and metagenomes

zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)

Some useful python scripts for biologists

An all-in-one genome-centric metagenomics workflow using long reads

VirNet: A deep attention model for viral reads identification

Spraynpray ⭐ 25

Rapid and simple taxonomic profiling of genome and metagenome contigs

tiara – a tool for DNA sequence classification

Args_oap ⭐ 24

ARGs-OAP: Online Analysis Pipeline for Antibiotic Resistance Genes Detection from Metagenomic Data Using an Integrated Structured ARG Database

Graphbin2 ⭐ 24

☯️🧬 Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs

Stag Mwc ⭐ 24

StaG Metagenomic Workflow Collaboration

Strainflair ⭐ 23

Strain-level abundances estimation in metagenomic samples using variation graphs

Lrbinner ⭐ 22

LRBinner is a long-read binning tool published in WABI 2021 proceedings and AMB.

Pathogentrack ⭐ 22

A pipeline to identify pathogenic microorganisms from scRNA-seq raw data.

Arg_ranker ⭐ 22

Binning_refiner ⭐ 22

Improving genome bins through the combination of different binning programs

Taxpasta ⭐ 21

TAXnomic Profile Aggregation and STAndardisation

Metagenomic binning based on Hi-C data

AMBER: Assessment of Metagenome BinnERs

A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly.

Pipelines ⭐ 20

Super Focus ⭐ 19

A tool for agile functional analysis of shotgun metagenomic data

Metameta ⭐ 18

Mapping-Assisted Targeted-Assembly for Metagenomics

2014 5 Metagenomics Workshop ⭐ 18

Metagenomics Workshop 2014-5-21 to 2014-5-23 at SciLifeLab, Stockholm

Whokaryote ⭐ 17

Classify metagenomic contigs as eukaryotic or prokaryotic

Reads For Assembly ⭐ 17

Simulate metagenomic short reads from one or more populations.

micca - MICrobial Community Analysis

Metscale ⭐ 16

MetScale: snakemake workflows to scale metagenome analyses

Metasub_cap ⭐ 16

A comprehensive pipeline for short read metagenomic data

Virstrain ⭐ 16

An RNA virus strain-level identification tool for short reads.

Metabcc Lr ⭐ 16

Reference-free Binning of Metagenomics Long Reads using Coverage and Composition

Hamroaster ⭐ 15

hAMRoaster is an analysis pipeline that can compare the output of nine different tools for detecting AMR genes and provide metrics of their performance

Snakemake workflow for comparison of differential abundance ranks

Set of tools for viral metagenomics.

Toolchest Client Python ⭐ 13

Toolchest Python client

Jaeger is an AI model for identifying phages in metagenome assemblies.

Query sequence database by HMMs arranged in predefined synteny structure

Flexible omics pipeline

Mdmcleaner ⭐ 13

MDMcleaner the assessment, classification and refinement tool for microbial dark matter SAGs and MAGs

Metagenomics_workflows ⭐ 13

Workflows for metagenomic sequence data processing and analysis.

Emg Toolkit ⭐ 13

MGnify API toolkit

AMR/VF LGT focused bacterial genomics analysis workflow

Metagenomics/viromics pipeline that focuses on automation, user-friendliness and a clear audit trail. Jovian aims to empower classical biologists and wet-lab personnel to do metagenomics/viromics analyses themselves, without bioinformatics expertise.

Living Oceans ⭐ 11

🌊 Robust workflows for gathering data about your local ocean.

MineYourSymbiont : Targetted genome assembly for metagenomics pipeline.

Snakemake based framework for NGS data analysis and management

Sequence Database Curator ⭐ 10

This program dereplicates and/or filter nucleotide and/or protein database from a list of names or sequences (by exact match).

Raspir, the rare species identifier

Phylogenetic Placement Evaluation Workflows : Benchmark placement software and different reference trees

Blast Filtering Pipeline ⭐ 10

A very simple BLAST filtering pipeline

Metafinishersc ⭐ 10

This tool is for users to upgrade their metagenomics assemblies using long reads. This includes fixing mis-assemblies and scaffolding/gap-filling.

Superpang ⭐ 9

Non-redundant pangenome assemblies from multiple genomes or bins

Cosmosid Cli ⭐ 9

Command line client and Python libraries for CosmosID API

Py Metagenomics ⭐ 9

Some python libs and scripts for metagenomic analyses

MGKit: Metagenomics Framework

Metagenomics Analysis ⭐ 8

Data Processing and Visualization for Metagenomics

Shotgun Metagenomics Pipeline ⭐ 8

A pipeline for primary analysis of shotgun metagenomic sequencing data

A simulator for horizontal gene transfer (HGT) in microbial communities

Notebooks ⭐ 8

MGnify documentation and Jupyter Lab notebooks to support downstream analysis of MGnify data (EMBL-EBI's metagenomics platform)

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

Findfungi ⭐ 7

A pipeline for the identification of fungi in public metagenomics datasets

Metassemble ⭐ 7

Scripts to run several metagenomics assembly programs

GDmicro - Use GCN and Deep adaptation network to classify host disease status based on human gut microbiome data.

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