metagenome

There are 1 repository under metagenome topic.

• smaegol / PlasFlow

  Software for prediction of plasmid sequences in metagenomic assemblies

  classificationcontigsfastametagenomemetagenome-assemblymetagenomesplasflowplasmidplasmid-sequencesplasmidspredictiontensorflow
  Language:Python 94

• Arkadiy-Garber / MagicLamp

  A platform for targeted annotation of (meta)genomic and (meta)transcriptomic datasets using HMM sets.

  hmmshmmerfegenieannotationgenomicsmetagenomeironmicrobialrespirationmagnetosomeslithogenielithotrophy
  Language:HTML 13

• franciscozorrilla / SymbNET

  Teaching materials for SymbNET course: from MAGs to GEMs

  metabolicmodelinggenomemodelsmetagenomeassembledgenomessymbnetmetagemmetabolism
  Language:Jupyter Notebook 12

• DMnBI / ViBE

  ViBE: a hierarchical BERT model to identify viruses using metagenome sequencing data

  transformersbertembeddingvirus-classificationmetagenomevirome
  Language:Python 7

• haradama / PlasmidPicker

  Software to identify plasmid sequence data from metagenome using logistic regression and Minhash

  plasmidsfastabioinformaticsmetagenomicsmetagenomecontigsminhashlogistic-regressionclassification
  Language:Python 6

• haradama / pHash

  Software to identify known plasmid sequence from metagenomic assembly using Minhash

  bioinformaticsfastametagenomicsmetagenomeminhashbiologyplasmidsplasmidcontigsgolang
  Language:Go 3

• TealFurnholm / Strain-Level_Metagenome_Analysis

  Using a universal reference database, mixed assemblies, and cutting-edge software to give you the quantitative community phylogeny, a complete community functional analysis, and many strain(ish)-level high-quality bins.

  metagenomemicrobiome-analysis
  Language:Perl 3

• JGI-Bioinformatics / axolotl

  Axolotl is a Python library for scalable genome analysis, addressing the gap in tools for handling the rapid growth of genomic data with easy parallel processing.

  axolotldistributed-computinggenomicsmetagenomepythonscalable
  Language:Python 2

• raw-lab / metaome_stats

  Statistical package for metaome denovo assembly results.

  metaome-statsfastagenomemetagenomemetagenome-assemblymetatranscriptomicstranscriptomics
  Language:Python 2

• suzuki-shm / GRiD-in-cwl

  Growth Rate Index Calculater wrapped by CWL

  cwl-workflowcwlbioinformaticsmetagenome
  Language:Common Workflow Language 1

• suzuki-shm / SPHERE

  Synthetic PHasE Rate Estimator by single metagenome sequence

  bioinformaticsmicrobiologygenomicspython3statisticsbayesian-inferencemetagenome
  Language:Python 1

• gundizalv / Arche

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

  annotationannotation-toolgenomegenome-annotationgenomesgenomicsmetagenomemetagenomesmetagenomics
  Language:Shell 0

• hildebra / clusterMAGs

  clutering of MAGs (metagenome assembled genomes) into MGS (metagenomic species)

  metagenomemetagenome-assembled-genomesmetagenome-binning
  Language:C++ 0

• mingleiR / trait-frame

  Microbial trait-based framework

  metagenometraits
  Language:HTML 0

• reslp / binner

  Run multiple metagenome filtering programs using Docker containers

  binnermetagenomeblobtoolsgenomemetagenome-assemblybuscoquastmultiqcmetabatmultiple-binners
  Language:Shell 0

• xvtyzn / MetaNyanko

  Shotgun metagenomic analysis pipeline for SGE

  metagenomenekocafe
  Language:Shell 0

• jiarong / rplB-metaG-pipeline

  rplB/rpsC targeted analyses with shotgun metagenomes

  rplbrpscmetagenomeassemblydiversity
  Language:Python