nf-core/mag

Assembly and binning of metagenomes

Language: Nextflow - Size: 19.3 MB - Last synced: 4 minutes ago - Pushed: about 1 hour ago - Stars: 183 - Forks: 97

cafferychen777/MicrobiomeStat

Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat

Language: R - Size: 15.7 MB - Last synced: about 22 hours ago - Pushed: 1 day ago - Stars: 24 - Forks: 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.

Size: 176 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 2 - Forks: 2

althonos/pyrodigal

Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!

Language: Cython - Size: 6.86 MB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 122 - Forks: 5

jtamames/SqueezeMeta

A complete pipeline for metagenomic analysis

Language: C - Size: 623 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 340 - Forks: 81

GenomicsStandardsConsortium/mixs

Minimum Information about any (X) Sequence” (MIxS) specification

Language: Python - Size: 372 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 33 - Forks: 20

gauravcodepro/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

Language: Shell - Size: 34.2 KB - Last synced: 9 days ago - Pushed: 14 days ago - Stars: 1 - Forks: 0

smaegol/PlasFlow

Software for prediction of plasmid sequences in metagenomic assemblies

Language: Python - Size: 37.7 MB - Last synced: 16 days ago - Pushed: almost 3 years ago - Stars: 89 - Forks: 27

althonos/pyfastani

Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.

Language: Cython - Size: 354 KB - Last synced: 25 days ago - Pushed: 3 months ago - Stars: 14 - Forks: 0

althonos/pyskani

PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.

Language: Rust - Size: 2.84 MB - Last synced: 20 days ago - Pushed: about 1 year ago - Stars: 17 - Forks: 0

marbl/MetaCarvel

MetaCarvel: A scaffolder for metagenomes

Language: C++ - Size: 6.11 MB - Last synced: about 2 months ago - Pushed: almost 3 years ago - Stars: 13 - Forks: 14

muellan/metacache

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

Language: C++ - Size: 149 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 55 - Forks: 10

mtisza1/Cenote-Taker2

Cenote-Taker2: Discover and Annotate Divergent Viral Contigs (Please use Cenote-Taker 3 instead)

Language: Shell - Size: 62.3 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 57 - Forks: 8

SegataLab/preprocessing

Raw sequence metagenomic reads pre-processing: trimming, QC, and host contamination

Language: Python - Size: 104 KB - Last synced: 4 months ago - Pushed: 6 months ago - Stars: 7 - Forks: 1

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.

Language: Perl - Size: 245 MB - Last synced: 7 months ago - Pushed: about 1 year ago - Stars: 22 - Forks: 5

raw937/SharkBay_metagenomes

Language: R - Size: 8.73 MB - Last synced: 7 months ago - Pushed: over 5 years ago - Stars: 1 - Forks: 0

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

Language: Python - Size: 7.34 MB - Last synced: 7 months ago - Pushed: about 3 years ago - Stars: 53 - Forks: 7

Chartiza/Microbiome

scripts for microbiome analysis

Language: HTML - Size: 23.6 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 10 - Forks: 2

Finesim97/MetaErgInstallHelper

A few scripts to help with the installation of MetaErg, the contig/bin annotation pipeline

Language: Shell - Size: 31.3 KB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 7 - Forks: 3

metageni/FOCUS

FOCUS: An Agile Profiler for Metagenomic Data

Language: Python - Size: 48.9 MB - Last synced: 18 days ago - Pushed: over 2 years ago - Stars: 7 - Forks: 8

SamStudio8/gretel

An algorithm for recovering haplotypes from metagenomes

Language: Python - Size: 780 KB - Last synced: 11 days ago - Pushed: almost 3 years ago - Stars: 31 - Forks: 4

xelanac/metagenomic-project

Application of Recurrent Neural Network to Metagenomic

Language: Jupyter Notebook - Size: 354 KB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 3 - Forks: 0

gundizalv/Arche

Arche: a functional-optimized annotator for microbial meta(genomes)

Language: Shell - Size: 131 KB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0

leylabmpi/animal_gut_metagenome_assembly

Code associated with the Ley Lab animal gut metagenome assembly project

Language: Jupyter Notebook - Size: 70.8 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 2 - Forks: 0

leylabmpi/MGSIM

Language: Python - Size: 5.51 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

lauralwd/Azolla_genus_metagenome

This project aims do describe and explore the metagenomes of fern species of the genus Azolla.

Language: Python - Size: 10.9 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 0

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

Language: C++ - Size: 127 MB - Last synced: about 1 year ago - Pushed: almost 7 years ago - Stars: 16 - Forks: 3

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

CAP Citrus Project for HLB

Size: 3.91 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

Reproducibility-FBB-MSU/CAMISIM_reproducibility

To reproduce some results from "CAMISIM: simulating metagenomes and microbial communities". Authors: Simon Konnov, Ciara Makievskaya, Ruslan Gumerov

Language: Jupyter Notebook - Size: 27.3 MB - Last synced: 12 months ago - Pushed: almost 5 years ago - Stars: 1 - Forks: 0

JotaKas/hmdb_scripts Fork of tmdb-team/tmdb

HumanMetagenomeDB: a public repository of curated and standardized metadata for human metagenomes

Language: Python - Size: 11.7 KB - Last synced: 3 months ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

suzuki-shm/DEMIC-in-cwl

CWL implementation for DEMIC

Language: Common Workflow Language - Size: 3.78 MB - Last synced: 29 days ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 0