Alternatives and similar repositories for taxonkit:

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

• oschwengers / bakta
  Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
  ☆474Updated this week
• jtamames / SqueezeMeta
  A complete pipeline for metagenomic analysis
  ☆392Updated last week
• MrOlm / drep
  Rapid comparison and dereplication of genomes
  ☆274Updated last month
• jenniferlu717 / KrakenTools
  KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
  ☆326Updated last year
• sanger-pathogens / Roary
  Rapid large-scale prokaryote pan genome analysis
  ☆329Updated 2 years ago
• 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…
  ☆374Updated last week
• metagenome-atlas / atlas
  ATLAS - Three commands to start analyzing your metagenome data
  ☆380Updated 3 weeks ago
• rrwick / Trycycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆314Updated 8 months ago
• nextgenusfs / funannotate
  Eukaryotic Genome Annotation Pipeline
  ☆330Updated last week
• Ecogenomics / CheckM
  Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
  ☆359Updated 4 months ago
• iqtree / iqtree2
  NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org
  ☆261Updated last week
• biobakery / MetaPhlAn
  MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
  ☆321Updated last week
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆215Updated 3 years ago
• bxlab / metaWRAP
  MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
  ☆412Updated last year
• jotech / gapseq
  Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks
  ☆169Updated this week
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆345Updated 2 years ago
• eggnogdb / eggnog-mapper
  Fast genome-wide functional annotation through orthology assignment
  ☆587Updated 8 months ago
• biobakery / biobakery
  bioBakery tools for meta'omic profiling
  ☆266Updated 3 months ago
• jenniferlu717 / Bracken
  Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species i…
  ☆299Updated 6 months ago
• arpcard / rgi
  Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on h…
  ☆345Updated last month
• TransDecoder / TransDecoder
  TransDecoder source
  ☆283Updated 3 months ago
• nf-core / mag
  Assembly and binning of metagenomes
  ☆226Updated this week
• ncbi / pgap
  NCBI Prokaryotic Genome Annotation Pipeline
  ☆326Updated last week
• nf-core / ampliseq
  Amplicon sequencing analysis workflow using DADA2 and QIIME2
  ☆190Updated this week
• edgardomortiz / vcf2phylip
  Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
  ☆303Updated last year
• tseemann / abricate
  Mass screening of contigs for antimicrobial and virulence genes
  ☆385Updated last year
• bioinformatics-centre / kaiju
  Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
  ☆276Updated 2 weeks ago
• MGXlab / CAT_pack
  CAT/BAT/RAT: tools for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) and for taxonomic profiling of metage…
  ☆201Updated last month
• tseemann / barrnap
  Bacterial ribosomal RNA predictor
  ☆232Updated last year
• gamcil / clinker
  Gene cluster comparison figure generator
  ☆551Updated 2 months ago