Alternatives and similar repositories for GTDBTk:

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

• oschwengers / bakta
  Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
  ☆492Updated 2 weeks ago
• Ecogenomics / CheckM
  Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
  ☆362Updated 6 months ago
• arpcard / rgi
  Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on h…
  ☆356Updated this week
• bxlab / metaWRAP
  MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
  ☆416Updated last year
• sanger-pathogens / Roary
  Rapid large-scale prokaryote pan genome analysis
  ☆338Updated 2 years ago
• tseemann / abricate
  Mass screening of contigs for antimicrobial and virulence genes
  ☆398Updated last year
• jtamames / SqueezeMeta
  A complete pipeline for metagenomic analysis
  ☆399Updated 2 weeks ago
• ncbi / pgap
  NCBI Prokaryotic Genome Annotation Pipeline
  ☆331Updated this week
• jenniferlu717 / Bracken
  Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species i…
  ☆304Updated last month
• metagenome-atlas / atlas
  ATLAS - Three commands to start analyzing your metagenome data
  ☆384Updated last week
• jenniferlu717 / KrakenTools
  KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
  ☆331Updated last year
• 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…
  ☆392Updated 2 months ago
• jiarong / VirSorter2
  customizable pipeline to identify viral sequences from (meta)genomic data
  ☆243Updated 4 months ago
• WrightonLabCSU / DRAM
  Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
  ☆268Updated this week
• biobakery / MetaPhlAn
  MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
  ☆331Updated last week
• MrOlm / drep
  Rapid comparison and dereplication of genomes
  ☆280Updated 3 months ago
• ParBLiSS / FastANI
  Fast Whole-Genome Similarity (ANI) Estimation
  ☆397Updated last year
• iqtree / iqtree2
  NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org
  ☆275Updated this week
• ncbi / amr
  AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and p…
  ☆298Updated last month
• mikolmogorov / Flye
  De novo assembler for single molecule sequencing reads using repeat graphs
  ☆819Updated 7 months ago
• rrwick / Unicycler
  hybrid assembly pipeline for bacterial genomes
  ☆586Updated 8 months ago
• hyattpd / Prodigal
  Prodigal Gene Prediction Software
  ☆473Updated last year
• nextgenusfs / funannotate
  Eukaryotic Genome Annotation Pipeline
  ☆339Updated 3 weeks ago
• shenwei356 / taxonkit
  A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
  ☆405Updated 2 weeks ago
• tseemann / mlst
  Scan contig files against PubMLST typing schemes
  ☆220Updated 2 years ago
• ablab / quast
  Genome assembly evaluation tool
  ☆421Updated 4 months ago
• rrwick / Trycycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆317Updated 10 months ago
• schneebergerlab / syri
  Synteny and Rearrangement Identifier
  ☆371Updated last month
• malonge / RagTag
  Tools for fast and flexible genome assembly scaffolding and improvement
  ☆499Updated last year
• tseemann / snippy
  Rapid haploid variant calling and core genome alignment
  ☆502Updated 8 months ago