metagenomic-analysis

There are 5 repositories under metagenomic-analysis topic.

ggpicrust2
cafferychen777 / ggpicrust2
Make Picrust2 Output Analysis and Visualization Easier
picrust2 functional-data metagenomic-analysis visualization tax4fun2 16s-rrna metagenomics microbiome microbiota
Language:R 97
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++ 57
MG-RAST / MG-RAST
The MG-RAST Backend -- the API server
metagenome-statistics metagenomic-analysis metagenomics
Language:Perl 44
vmikk / metagMisc
Miscellaneous functions for metagenomic analysis.
metagenomic-analysis parser r
Language:R 44
katerinakazantseva / strainy
Graph-based assembly phasing
assembly hifi long-read-sequencing long-reads metagenomic-analysis metagenomics nanopore sequencing
Language:Python 41
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 30
anuradhawick / LRBinner
LRBinner is a long-read binning tool published in WABI 2021 proceedings and AMB.
bioinformatics metagenomics metagenomic-analysis metagenomics-binning python pacbio nanopore-sequencing
Language:Python 28
ctmrbio / stag-mwc
StaG Metagenomic Workflow Collaboration
snakemake-workflows metagenomic-analysis metagenomics research microbiome
Language:Python 26
MG-RAST / pipeline
The MG-RAST pipeline
metagenomic-analysis
Language:Common Workflow Language 24
GreyGuoweiChen / VirBot
VirBot: a protein-based RNA virus detector for metagenomic data
bioinformatics hmm-model metagenomic-analysis rna-virus
Language:Python 23
SchulzLab / ORNA
Fast in-silico normalization algorithm for NGS data
ngstools normalization rna-seq metagenomics metagenomic-analysis rna-seq-analysis
Language:C++ 22
EBI-Metagenomics / pipeline-v5
This repository contains all CWL descriptions of the MGnify pipeline version 5.0.
common-workflow-language cwl workflow cwl-descriptions cwl-workflow mgnify metagenomic-pipeline metagenomic-analysis metagenomic-classification metagenomic-data metagenomics amplicon-pipeline wgs-analysis
Language:HTML 21
Ivarz / Conifer
Calculate confidence scores from Kraken2 output
kraken2 confidence-scores metagenomic-analysis
Language:C 18
pnnl / mercat
MerCat: python code for versatile k-mer counting and diversity estimation for database independent property analysis for meta -ome data
metagenomic-analysis metatranscriptomic-analysis kmer-frequency-count plotly diversity divideandconquer python dask k-mer-counting k-mer-frequency protein nucleotides fastq diversity-estimation database-independent-analysis
Language:Python 18
treangenlab / lemur
Lemur is a tool for rapid and accurate taxonomic profiling on long-read metagenomic datasets
long-read-sequencing long-reads metagenomic-analysis metagenomic-classification metagenomics taxonomic-classification taxonomic-profiling
Language:Python 16
anuradhawick / seq2vec
Fast sequence vectorization for metagenomics analysis. Converts input sequences into oligonucleotide frequency vectors, fast!
bioinformatics bioinformatics-tool metagenomics metagenomics-binning metagenomic-analysis
Language:C++ 14
tmbuza / iMAP
iMAP v1.0 (Pre-release): Integrated Microbiome Analysis Pipeline
16s-rrna metagenomic-analysis microbiome-analysis visualization
Language:HTML 14
CMU-SAFARI / Genome-on-Diet
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).
genome-analysis read-mapping variant-calling containment-search genomics large-scale metagenomic-analysis metagenomics microbiome-analysis sequence-alignment wavefront-alignment bioinformatics minimap2 genome-on-diet
Language:Roff 11
mmpust / raspir
Raspir, the rare species identifier
rare-species metagenomics fourier-transform metagenomic-analysis species-identification python3
Language:Python 11
raw-lab / mercat2
MerCat2: python code for versatile k-mer counting and diversity estimation for database independent property analysis for metaome data
python diversity plotly multiomics multiomics-data protein dask fastq k-mer-counting k-mer-frequency divideandconquer metagenomic-analysis metatranscriptomic-analysis kmer-frequency-count nucleotides diversity-estimation database-independent-analysis
Language:HTML 11
snz20 / carnelian
metagenomic-analysis functional-binning
Language:Python 11
new-atlantis-labs / Metagenomics
🐋 The Living Oceans Metagenome Taxanomic Profiling tool (beta) is a metagenomic pipeine built to work on your local ocean
bioinformatics bioinformatics-pipeline python python3 metagenomic-analysis metagenomic-pipeline metagenomics plankton gitcoin ocean desci gitcoin-grants resci
Language:Jupyter Notebook 7
pjtorres / metagenomics_tutorial
Analyzing shotgun data
docker metaphlan bowtie metagenomic-analysis quality-control
Language:HTML 6
pfeiferd / genestrip
Genestrip - Efficient read classification, filtering and k-mer counting for selected groups of species
bioinformatics genomes genomic-data-analysis high-performance kmer-counting kraken2 krakenuniq metagenomic-analysis metagenomic-classification pathogen-genomics command-line-tool java
Language:Java 5
QuentinLetourneur / Let-it-bin
Optimize workflow for binning metagenomic short reads from multiple samples
nextflow binning metagenomic-analysis singularity-containers
Language:Nextflow 5
rusher321 / rmeta
collect the R function for daily work
rmeta r metagenomic-analysis
Language:HTML 5
treangenlab / komb
KOMB is a tool for fast identification of unitigs of interest in metagenomes. KOMB introduces the concept of a Hybrid Unitig Graph (an extension to compacted de Bruijn graphs) and relies on k-core and K-truss decomposition algorithms.
anomaly-detection k-core-decomposition metagenomic-analysis metagenomic-pipeline metagenomics short-read-sequencing
Language:C++ 5
ac1513 / MAGqual
MAGqual is a command line tool to evaluate the quality of metagenomic bins and generate recommended metadata in line with the MIMAG standards
metagenomic-analysis metagenomic-pipeline metagenomics snakemake snakemake-pipeline
Language:Python 4
CMU-SAFARI / MetaTrinity
MetaTrinity is a novel metagenomic analysis tool employing efficient containment search techniques and heuristics for read mapping to achieve significant speedup while maintaining high accuracy. This positions MetaTrinity as an efficient solution, optimally balancing speed and precision in metagenomic analysis.
clinical-research containment-search genomics medical-application metagenomic-analysis metagenomics microbiome-analysis readmapping
Language:HTML 4
MattCzajkowski / GenCoF
A graphical user interface for a genomic contamination filtering pipeline to filter out reads from metagenomic files
bioinformatics gui contamination-filtering metagenomic-analysis
Language:C++ 4
sipost1 / kraken2OTUtable
Creates a simple OTU table from Kraken2 report.
bioinformatics metagenomics metagenomic-analysis kraken2 otu-table commmand-line data-analysis bracken python3
Language:Python 4
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
3
Geomosaic
giovannellilab / Geomosaic
A flexible metagenomic pipeline combining read-based, assemblies and MAGs with downstream analysis
metagenomics microbial-communities metagenomic-analysis metagenomic-pipeline pipeline wgs whole-genome-sequencing customizable
Language:Python 3
hivlab / discover-virome
discover-virome: identify and quantify viruses from metagenomic assemblies
virome virome-workflow snakemake snakemake-workflow metagenomic-analysis metagenomic-classification
Language:Python 3
ZiyueYang01 / Phyrvm
Phyrvm: A one-stop software solution for RNA virus mining and host-association prediction
bioinformatics host-association metagenomic-analysis rna-virus
Language:Python 3
bo1929 / CONSULT-II
Accurate taxonomic classification and abundance profiling using locality-sensitive hashing.
taxonomic-classification contamination-removal metagenomic-analysis metagenomic-classification metagenomics
Language:C++ 2