Alternatives and similar repositories for gtdb_to_taxdump:

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

• rrwick / Metagenomics-Index-Correction
  ☆81Updated last year
• shenwei356 / gtdb-taxdump
  GTDB taxonomy taxdump files with trackable TaxIds
  ☆52Updated 11 months ago
• hzi-bifo / traitar
  From genomes to phenotypes: Traitar, the microbial trait analyzer
  ☆59Updated 5 years ago
• christophertbrown / iRep
  scripts for estimating bacteria replication rates based on population genome copy number variation
  ☆72Updated 5 years ago
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆76Updated 3 years ago
• jhawkey / IS_mapper
  IS mapping software
  ☆53Updated 3 years ago
• gbouras13 / dnaapler
  Reorients assembled microbial sequences
  ☆116Updated 2 weeks ago
• geronimp / graftM
  GraftM - Rapid community profiles from metagenomes
  ☆45Updated 8 months ago
• DeniRibicic / q2ONT
  Bash pipeline for analysis of ONT full-length 16S sequences in QIIME2
  ☆29Updated 5 years ago
• lmrodriguezr / nonpareil
  Estimate metagenomic coverage and sequence diversity
  ☆48Updated 8 months ago
• gtonkinhill / panstripe
  post processing of bacterial pangenome gene presence/absence matrices
  ☆59Updated last month
• patrickwest / EukRep
  Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets
  ☆69Updated 9 months ago
• songweizhi / MetaCHIP
  Horizontal gene transfer (HGT) identification pipeline
  ☆57Updated last year
• linsalrob / PhiSpy
  Prediction of prophages from bacterial genomes
  ☆77Updated last year
• KatariinaParnanen / MobileGeneticElementDatabase
  Contains a fasta format database of a large variety of mobile genetic elements and an annotation file
  ☆46Updated 3 years ago
• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆71Updated last year
• transcript / samsa2
  SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…
  ☆57Updated last year
• moshi4 / ANIclustermap
  A tool for drawing ANI clustermap between all-vs-all microbial genomes
  ☆76Updated 7 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…
  ☆54Updated 3 years ago
• gbouras13 / hybracter
  Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.
  ☆124Updated last month
• bjtully / BioData
  All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")
  ☆72Updated 2 years ago
• Hydro3639 / NanoPhase
  Reference-quality genome reconstruction from complex metagenomes (or bacterial isolates) using only Nanopore long reads or both long and …
  ☆32Updated last year
• biofuture / Ublastx_stageone
  This is the source code for multisamples ARGs profiling using SARG2.0 database
  ☆46Updated 4 years ago
• allind / EukDetect
  ☆50Updated last year
• WatsonLab / MAGpy
  Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
  ☆62Updated 2 years ago
• nigyta / dfast_core
  DDBJ Fast Annotation and Submission Tool
  ☆79Updated last month
• nekokoe / Plasmer
  An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features.
  ☆43Updated last year
• moshi4 / COGclassifier
  A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category
  ☆62Updated 7 months ago
• ablab / viralVerify
  viralVerify: viral contig verification tool
  ☆67Updated 3 years ago
• Finn-Lab / MAG_Snakemake_wf
  Recovery of prokaryotic genomes from shotgun metagenomic sequencing data
  ☆59Updated 3 years ago