Alternatives and similar repositories for MetaPhlAn2

Users that are interested in MetaPhlAn2 are comparing it to the libraries listed below

• bhattlab / kraken2_classification
  Snakemake workflow for metagenomic classification with Kraken2
  ☆65Updated 2 years ago
• transcript / samsa2
  SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…
  ☆56Updated last year
• grimmlab / MicrobiomeBestPracticeReview
  Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
  ☆120Updated last year
• ohmeta / metapi
  A general metagenomics data mining system focus on robust microbiome research
  ☆58Updated last year
• HCBravoLab / metagenomeSeq
  Statistical analysis for sparse high-throughput sequencing
  ☆69Updated 9 months ago
• victoriapascal / gutsmash
  gutSMASH
  ☆55Updated 9 months ago
• karkman / MetagenomeCourse2019
  Course material for the metagenomics course
  ☆44Updated 3 years ago
• bjtully / BioData
  All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")
  ☆77Updated 2 years ago
• nf-core / bacass
  Simple bacterial assembly and annotation pipeline
  ☆77Updated 2 weeks ago
• AstrobioMike / bit
  Bioinformatics Tools
  ☆89Updated 3 weeks ago
• SegataLab / lefse
  ☆84Updated last year
• biobakery / biobakery_workflows
  bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validate…
  ☆117Updated 3 months ago
• husonlab / megan-ce
  MEGAN Community Edition
  ☆72Updated last year
• bokulich-lab / RESCRIPt
  REference Sequence annotation and CuRatIon Pipeline
  ☆97Updated 2 weeks ago
• ParkinsonLab / Metatranscriptome-Workshop
  Metatranscriptomics Tutorial
  ☆63Updated 2 years ago
• hzi-bifo / RiboDetector
  Accurate and rapid RiboRNA sequences Detector based on deep learning
  ☆115Updated last year
• nf-core / funcscan
  (Meta-)genome screening for functional and natural product gene sequences
  ☆91Updated last week
• nvelden / geneviewer
  An R package designed for drawing gene arrow maps
  ☆88Updated 2 months ago
• smdabdoub / kraken-biom
  Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…
  ☆55Updated 3 years ago
• Sydney-Informatics-Hub / Shotgun-Metagenomics-Analysis
  Analysis of metagenomic shotgun sequences including assembly, speciation, ARG discovery and more
  ☆35Updated 2 years ago
• mjsull / Easyfig
  Development version of Easyfig
  ☆100Updated last year
• biobakery / kneaddata
  Quality control tool on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.
  ☆130Updated last month
• PacificBiosciences / HiFi-16S-workflow
  Nextflow pipeline to analyze PacBio HiFi full-length 16S data
  ☆83Updated 2 months ago
• Zymo-Research / figaro
  An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters
  ☆90Updated last year
• scwatts / fastspar
  Rapid and scalable correlation estimation for compositional data
  ☆92Updated last year
• arumugamlab / msamtools
  Metagenomics-related extended functionalities to samtools
  ☆21Updated 2 years ago
• MicrobeLab / DeepMicrobes
  DeepMicrobes: taxonomic classification for metagenomics with deep learning
  ☆100Updated 3 years ago
• hzi-bifo / traitar
  From genomes to phenotypes: Traitar, the microbial trait analyzer
  ☆60Updated 6 years ago
• nmquijada / tormes
  Making whole bacterial genome sequencing data analysis easy
  ☆110Updated 5 months ago
• nearinj / Comparison_of_DA_microbiome_methods
  ☆56Updated last year