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Search results for bioinformatics metagenomics
bioinformatics
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metagenomics
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114 search results found
Mmseqs2
⭐
1,235
MMseqs2: ultra fast and sensitive search and clustering suite
Vsearch
⭐
605
Versatile open-source tool for microbiome analysis
Megahit
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442
Ultra-fast and memory-efficient (meta-)genome assembler
Dada2
⭐
428
Accurate sample inference from amplicon data with single nucleotide resolution
Anvio
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396
An analysis and visualization platform for 'omics data
Gtdbtk
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383
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
Kaiju
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236
Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
Dram
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214
Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
Krakenuniq
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201
🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results
Drep
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199
Rapid comparison and dereplication of genomes
Mag
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164
Assembly and binning of metagenomes
Insilicoseq
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158
🚀 A sequencing simulator
Metagem
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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
Metaeuk
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142
MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics
Ngless
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141
NGLess: NGS with less work
Computationalgenomicsmanual
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135
Robs manual for the computational genomics and bioinformatics class.
Decontam
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122
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
Dnanalyzer
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122
Revolutionizing DNA analysis and making it accessible to all through innovative AI-powered analysis and interpretive tools
Eager
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112
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
Spacegraphcats
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112
Indexing & querying large assembly graphs -- in space, no one can hear you miao!
Rapdtool
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110
Rapid Profiling and Deconvolution Tool for Metagenomes
Skani
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101
Fast, robust ANI and aligned fraction for metagenomic genomes and contigs.
Plass
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99
Protein-Level ASSembler (PLASS): sensitive and precise protein assembler
Semibin
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89
SemiBin: metagenomics binning with self-supervised deep learning
Taxprofiler
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78
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Czid Web
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75
Infectious Disease Sequencing Platform
Ganon
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73
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
Lambda
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70
LAMBDA – the Local Aligner for Massive Biological DatA
Bonsai
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68
Bonsai: Fast, flexible taxonomic analysis and classification
Catch
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63
A package for designing compact and comprehensive capture probe sets.
Aviary
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62
A hybrid assembly and MAG recovery pipeline (and more!)
Deepmicrobes
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61
DeepMicrobes: taxonomic classification for metagenomics with deep learning
Woltka
⭐
58
Woltka: a versatile meta'omic data classifier
Phables
⭐
56
🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes
Fastv
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56
An ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. This tool can be used to detect viral infectious diseases, like COVID-19.
Metabuli
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54
Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.
Flashweave.jl
⭐
52
Inference of microbial interaction networks from large-scale heterogeneous abundance data
Metacache
⭐
49
memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping
Funcscan
⭐
49
(Meta-)genome screening for functional and natural product gene sequences
Macrel
⭐
48
Predict AMPs in (meta)genomes and peptides
Gecco
⭐
45
GEne Cluster prediction with COnditional random fields.
Microbiomebestpracticereview
⭐
45
Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
Grabseqs
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44
A utility for easy downloading of reads from next-gen sequencing repositories like NCBI SRA
Metachip
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42
Horizontal gene transfer (HGT) identification pipeline
Panphlan
⭐
38
PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
Traitar
⭐
34
From genomes to phenotypes: Traitar, the microbial trait analyzer
Kraken Biom
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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
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32
Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.
Charcoal
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31
Remove contaminated contigs from genomes using k-mers and taxonomies.
Prophyle
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30
Accurate, resource-frugal and deterministic DNA sequence classifier.
Wochenende
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30
Deprecated see https://github.com/MHH-RCUG/nf_wochenende : A whole Genome/Metagenome Sequencing Alignment Pipeline in Python3
Nonpareil
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29
Estimate metagenomic coverage and sequence diversity
Zol
⭐
28
zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
Bio Py
⭐
27
Some useful python scripts for biologists
Virnet
⭐
26
VirNet: A deep attention model for viral reads identification
Mmlong2
⭐
26
An all-in-one genome-centric metagenomics workflow using long reads
Tiara
⭐
25
tiara – a tool for DNA sequence classification
Lrbinner
⭐
22
LRBinner is a long-read binning tool published in WABI 2021 proceedings and AMB.
Binning_refiner
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22
Improving genome bins through the combination of different binning programs
Metagenomescope
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22
Visualization tool for (meta)genome assembly graphs
Pathogentrack
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22
A pipeline to identify pathogenic microorganisms from scRNA-seq raw data.
Taxpasta
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21
TAXnomic Profile Aggregation and STAndardisation
Assemblycomparator2
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20
🦠📇 Compare prokaryotic genomic assemblies
Partie
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20
PARTIE is a program to partition sequence read archive (SRA) metagenomics data into amplicon and shotgun data sets. The user-supplied annotations of the data sets can not be trusted, and so PARTIE allows automatic separation of the data.
Vizbin
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20
Repository of our application for human-augmented binning
Course2017
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20
Genomics lessons for week 4 of the Microbial Diversity course at the Marine Biological Lab in Woods Hole, MA.
Metacherchant
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19
Super Focus
⭐
19
A tool for agile functional analysis of shotgun metagenomic data
Matam
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18
Mapping-Assisted Targeted-Assembly for Metagenomics
Vircov
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18
Viral genome coverage evaluation for metagenomic diagnostics 🩸
Whokaryote
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17
Classify metagenomic contigs as eukaryotic or prokaryotic
Microbiomer
⭐
17
A comprehensive R package for microbiome analysis.
Metasub_cap
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16
A comprehensive pipeline for short read metagenomic data
Micca
⭐
16
micca - MICrobial Community Analysis
Hamroaster
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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
Snikt
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14
Sequence-independent identification and removal of adapters/systemic contamination in shotgun sequencing data. https://doi.org/10.1093/bioinformatics/btac389
Pynteny
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13
Query sequence database by HMMs arranged in predefined synteny structure
Mdmcleaner
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13
MDMcleaner the assessment, classification and refinement tool for microbial dark matter SAGs and MAGs
Ymp
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13
Flexible omics pipeline
Emg Toolkit
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13
MGnify API toolkit
Qadabra
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13
Snakemake workflow for comparison of differential abundance ranks
Functree Ng
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13
An interactive radial tree for functional hierarchies and omics data visualization
Taxor
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13
Fast and space-efficient taxonomic classification of long reads
Toolchest Client Python
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13
Toolchest Python client
Virmet
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13
Set of tools for viral metagenomics.
Living Oceans
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11
🌊 Robust workflows for gathering data about your local ocean.
Genome On Diet
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11
Genome-on-Diet is a fast and memory-frugal framework for exemplifying sparsified genomics for read mapping, containment search, and metagenomic profiling. It is much faster & more memory-efficient than minimap2 for Illumina, HiFi, and ONT reads. Described by Alser et al. (preliminary version: https://arxiv.org/abs/2211.08157).
Bioinformatics Toolbox
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10
Docker container for bioinformatics tools and pipelines
Sequence Database Curator
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10
This program dereplicates and/or filter nucleotide and/or protein database from a list of names or sequences (by exact match).
Raspir
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10
Raspir, the rare species identifier
Bioinformatics
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10
A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common DNA and RNA sequence analysis methods.
Ng Meta Profiler
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10
Profiler for metagenomics based on NGLess
Superpang
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9
Non-redundant pangenome assemblies from multiple genomes or bins
Mgkit
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8
MGKit: Metagenomics Framework
Despi
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8
fast classification of metagenomic sequences with lightweight de Bruijin graph-based reference indexing
Hgtsim
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8
A simulator for horizontal gene transfer (HGT) in microbial communities
Famli
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8
Functional Analysis of Metagenomes by Likelihood Inference
Viralcc
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8
ViralCC: leveraging metagenomic proximity-ligation to retrieve complete viral genomes
Metacrast
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8
MetaCRAST: reference-guided CRISPR detection in metagenomes
Pydamage
⭐
7
Damage parameter estimation for ancient DNA
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