Alternatives and similar repositories for MetaPhlAn

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

• biobakery / biobakery
  bioBakery tools for meta'omic profiling
  ☆283Updated last month
• Ecogenomics / CheckM
  Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
  ☆376Updated last month
• bxlab / metaWRAP
  MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
  ☆430Updated last year
• jenniferlu717 / KrakenTools
  KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
  ☆345Updated last year
• biobakery / humann
  HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).
  ☆203Updated 11 months ago
• nextgenusfs / funannotate
  Eukaryotic Genome Annotation Pipeline
  ☆356Updated last week
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆235Updated 4 years ago
• jtamames / SqueezeMeta
  A complete pipeline for metagenomic analysis
  ☆421Updated last week
• tseemann / abricate
  Mass screening of contigs for antimicrobial and virulence genes
  ☆428Updated last year
• ncbi / pgap
  NCBI Prokaryotic Genome Annotation Pipeline
  ☆342Updated last month
• sanger-pathogens / Roary
  Rapid large-scale prokaryote pan genome analysis
  ☆354Updated 3 years ago
• oschwengers / bakta
  Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
  ☆532Updated last week
• usadellab / Trimmomatic
  ☆256Updated last year
• jiarong / VirSorter2
  customizable pipeline to identify viral sequences from (meta)genomic data
  ☆260Updated 7 months ago
• arpcard / rgi
  Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on h…
  ☆375Updated last month
• Gaius-Augustus / BRAKER
  BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eu…
  ☆416Updated 5 months ago
• rrwick / Trycycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆325Updated last year
• rrwick / Porechop
  adapter trimmer for Oxford Nanopore reads
  ☆365Updated last year
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆367Updated 3 years ago
• jenniferlu717 / Bracken
  Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species i…
  ☆311Updated 4 months ago
• picrust / picrust2
  Code, unit tests, and tutorials for running PICRUSt2
  ☆361Updated 3 months ago
• tseemann / mlst
  Scan contig files against PubMLST typing schemes
  ☆238Updated 2 years ago
• ablab / quast
  Genome assembly evaluation tool
  ☆445Updated 8 months ago
• tseemann / barrnap
  Bacterial ribosomal RNA predictor
  ☆247Updated last year
• MrOlm / drep
  Rapid comparison and dereplication of genomes
  ☆302Updated last month
• gtonkinhill / panaroo
  An updated pipeline for pangenome investigation
  ☆306Updated 4 months ago
• nf-core / mag
  Assembly and binning of metagenomes
  ☆241Updated last week
• franciscozorrilla / metaGEM
  An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within micro…
  ☆242Updated 11 months ago
• metagenome-atlas / atlas
  ATLAS - Three commands to start analyzing your metagenome data
  ☆393Updated 2 months ago
• TransDecoder / TransDecoder
  TransDecoder source
  ☆292Updated 9 months ago