metagenomes

There are 1 repository under metagenomes topic.

jtamames / SqueezeMeta
A complete pipeline for metagenomic analysis
metagenomics pipeline metagenomes taxonomic-assignment
Language:C 343
nf-core / mag
Assembly and binning of metagenomes
workflow nextflow metagenomics assembly binning annotation nf-core pipeline bioinformatics nanopore nanopore-sequencing metagenomes long-read-sequencing
Language:Nextflow 182
althonos / pyrodigal
Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!
orf-finder metagenomes python bioconda python-library cython-wrapper python-interface prodigal genome gene-finding bioinformatics simd
Language:Cython 122
smaegol / PlasFlow
Software for prediction of plasmid sequences in metagenomic assemblies
classification prediction contigs plasmid fasta plasmid-sequences tensorflow metagenome-assembly metagenome metagenomes plasmids plasflow
Language:Python 92
Shamir-Lab / Recycler
This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye Rozov, Aya Brown Kav, David Bogumil, Naama Shterzer, Eran Halperin, Itzhak Mizrahi, and Ron Shamir
assembly-graph plasmid metagenomes recycler denovo assembly circular-sequences
Language:Python 58
mtisza1 / Cenote-Taker2
Cenote-Taker2: Discover and Annotate Divergent Viral Contigs (Please use Cenote-Taker 3 instead)
cenote-taker2 metagenomes annotation genbank virus virome hhsearch hhblits discovery hallmark virus-discovery virus-sequences cenote-unlimited-breadsticks virus-evolution prophage prophage-prediction
Language:Shell 57
muellan / metacache
memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping
genome read-mapping refseq taxonomy metagenomics metagenomic-analysis metagenomic-classification metagenomes metagenomic-data ncbi-refseq fasta fastq dna-sequences genomic-data-analysis classification bioinformatics bioinformatics-tool bioinformatics-algorithms short-read-mapper long-reads
Language:C++ 55
GenomicsStandardsConsortium / mixs
Minimum Information about any (X) Sequence” (MIxS) specification
contextual-data gsc json-schema standard metagenomes genomics bioinformatics
Language:Python 33
SamStudio8 / gretel
An algorithm for recovering haplotypes from metagenomes
bioinformatics haplotypes metagenomes
Language:Python 31
cafferychen777 / MicrobiomeStat
Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat
16s-rrna amplicon-sequencing dada2 longitudinal-data metagenomes metagenomic-analysis microbiome microbiome-analysis microbiome-data phyloseq qiime2 statistics visualization microbiome-workflow omics omics-data-integration
Language:R 24
linsalrob / partie
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.
bioinformatics sra metagenomic-data metagenomics metagenomes
Language:Perl 24
Shamir-Lab / Faucet
This is the codebase for Faucet, described in our manuscript: https://academic.oup.com/bioinformatics/article/34/1/147/4004871, by Roye Rozov, Gil Goldshlager, Eran Halperin, and Ron Shamir
metagenomes streaming-algorithms de-novo-assembly
Language:C++ 18
althonos / pyskani
PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.
bioinformatics taxonomy ani average-nucleotide-identity metagenomes python-bindings python-library
Language:Rust 17
althonos / pyfastani
Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.
bioinformatics python-library python-bindings cython-library metagenomes average-nucleotide-identity taxonomy ani
Language:Cython 15
marbl / MetaCarvel
MetaCarvel: A scaffolder for metagenomes
genome-assembly metagenomes scaffolder
Language:C++ 13
Microbiome
Chartiza / Microbiome
scripts for microbiome analysis
metagenomes microbiome wgs-data
Language:HTML 11
SegataLab / preprocessing
Raw sequence metagenomic reads pre-processing: trimming, QC, and host contamination
preprocessing raw-reads metagenomes python tools
Language:Python 8
metageni / FOCUS
FOCUS: An Agile Profiler for Metagenomic Data
bioinformatics identify-organisms kmer metagenomes microbiome
Language:Python 7
Finesim97 / MetaErgInstallHelper
A few scripts to help with the installation of MetaErg, the contig/bin annotation pipeline
metagenomic-pipeline metagenomes annotation
Language:Shell 6
zoubohao / Deepurify
Deepurify is a tool to filter the contaminated contigs in a MAG with a language model.
metagenomes
Language:Python 6
xelanac / metagenomic-project
Application of Recurrent Neural Network to Metagenomic
lstm deep-learning neural-network machine-learning tensorflow keras metagenomes nlp python recurrent-neural-networks
Language:Jupyter Notebook 3
cafferychen777 / MicrobiomeStat-Turtorial-Professional-Version
MicrobiomeStat Tutorial Repository: This is a comprehensive resource for learning how to use the MicrobiomeStat package. It provides a step-by-step guide to effectively analyze complex microbiome data.
16s 16s-rrna 16s-seq analysis data-analysis metagenomes metagenomic-analysis metagenomic-pipeline metagenomics microbiome microbiome-analysis microbiome-analysis-pipelines microbiome-data microbiome-workflow omics omics-data omics-data-analysis omics-data-integration visualization
2
leylabmpi / animal_gut_metagenome_assembly
Code associated with the Ley Lab animal gut metagenome assembly project
bioinformatics metagenome-assembly metagenomes research-project
Language:Jupyter Notebook 2
gauravearn / pangenomes-metagenomes
a workflow for complete analysis of bacterial metagenomes and pagenome graphs and direct viewing in panchae. It will also analyze metagenomes from both illumina and long reads
bacterial-genomes bioinformatics metagenomes metagenomics-data pangenomics pangraphs
Language:Shell 1
lauralwd / Azolla_genus_metagenome
This project aims do describe and explore the metagenomes of fern species of the genus Azolla.
azolla symbiosis metagenomes plant metagenomics metagenomic-pipeline metagenome-assembly snakemake conda bioconda bioinformatics bioinformatics-pipeline biological-data-analysis fair-data endophytes symbiont
Language:Python 1
raw937 / SharkBay_metagenomes
microbialites stromatolites metagenomics metagenomes
Language:R 1
Reproducibility-FBB-MSU / CAMISIM_reproducibility
To reproduce some results from "CAMISIM: simulating metagenomes and microbial communities". Authors: Simon Konnov, Ciara Makievskaya, Ruslan Gumerov
camisim metagenomes reproducibility
Language:Jupyter Notebook 1
Citrus-HLB-Micro / Citrus-HLB-Micro.github.io
CAP Citrus Project for HLB
citrus genomics microbiome metagenomes
0
gundizalv / Arche
Arche: a functional-optimized annotator for microbial meta(genomes)
annotation annotation-tool genomes genomics metagenomes metagenomics genome genome-annotation metagenome
Language:Shell 0
JotaKas / hmdb_scripts
HumanMetagenomeDB: a public repository of curated and standardized metadata for human metagenomes
metagenomes human-metagenome sra-data mg-rast-data metadata
Language:Python 0
Tharos-ux / wisp
XGBoost implementation for bacteria family identification
classification metagenomes metagenomic-analysis metagenomic-classification metagenomics phylogenetics phylogeny
Language:Python 0
leylabmpi / MGSIM
genomes metagenomes simulations
Language:Python
suzuki-shm / DEMIC-in-cwl
CWL implementation for DEMIC
cwl bioinformatics metagenomes
Language:Common Workflow Language

metagenomes

jtamames / SqueezeMeta

nf-core / mag

althonos / pyrodigal

smaegol / PlasFlow

Shamir-Lab / Recycler

mtisza1 / Cenote-Taker2

muellan / metacache

GenomicsStandardsConsortium / mixs

SamStudio8 / gretel

cafferychen777 / MicrobiomeStat

linsalrob / partie

Shamir-Lab / Faucet

althonos / pyskani

althonos / pyfastani

marbl / MetaCarvel

Chartiza / Microbiome

SegataLab / preprocessing

metageni / FOCUS

Finesim97 / MetaErgInstallHelper

zoubohao / Deepurify

xelanac / metagenomic-project

cafferychen777 / MicrobiomeStat-Turtorial-Professional-Version

leylabmpi / animal_gut_metagenome_assembly

gauravearn / pangenomes-metagenomes

lauralwd / Azolla_genus_metagenome

raw937 / SharkBay_metagenomes

Reproducibility-FBB-MSU / CAMISIM_reproducibility

Citrus-HLB-Micro / Citrus-HLB-Micro.github.io

gundizalv / Arche

JotaKas / hmdb_scripts

Tharos-ux / wisp

leylabmpi / MGSIM

suzuki-shm / DEMIC-in-cwl