Alternatives and similar repositories for qiime2

Users that are interested in qiime2 are comparing it to the libraries listed below

• jtamames / SqueezeMeta
  A complete pipeline for metagenomic analysis
  ☆435Updated last month
• DerrickWood / kraken2
  The second version of the Kraken taxonomic sequence classification system
  ☆837Updated 2 weeks ago
• eggnogdb / eggnog-mapper
  Fast genome-wide functional annotation through orthology assignment
  ☆664Updated 4 months ago
• rrwick / Unicycler
  hybrid assembly pipeline for bacterial genomes
  ☆623Updated last year
• davidemms / OrthoFinder
  Phylogenetic orthology inference for comparative genomics
  ☆803Updated 3 months ago
• gamcil / clinker
  Gene cluster comparison figure generator
  ☆620Updated 11 months ago
• LangilleLab / microbiome_helper
  A repository of bioinformatic scripts, SOPs, and tutorials for analyzing microbiome data.
  ☆453Updated 10 months ago
• oschwengers / bakta
  Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
  ☆561Updated last week
• tseemann / prokka
  Rapid prokaryotic genome annotation
  ☆938Updated last year
• benjjneb / dada2
  Accurate sample inference from amplicon data with single nucleotide resolution
  ☆523Updated 3 months ago
• picrust / picrust2
  Code, unit tests, and tutorials for running PICRUSt2
  ☆371Updated last week
• biobakery / biobakery
  bioBakery tools for meta'omic profiling
  ☆288Updated 4 months ago
• bxlab / metaWRAP
  MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
  ☆445Updated 2 years ago
• bactopia / bactopia
  A flexible pipeline for complete analysis of bacterial genomes
  ☆480Updated last week
• marbl / Krona
  Interactively explore metagenomes and more from a web browser.
  ☆490Updated 3 years ago
• fbreitwieser / pavian
  🌈 Interactive analysis of metagenomics data
  ☆427Updated last month
• ablab / quast
  Genome assembly evaluation tool
  ☆468Updated 11 months ago
• Ecogenomics / CheckM
  Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
  ☆392Updated 4 months ago
• biobakery / MetaPhlAn
  MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
  ☆373Updated last week
• tseemann / abricate
  Mass screening of contigs for antimicrobial and virulence genes
  ☆444Updated last year
• metagenome-atlas / atlas
  ATLAS - Three commands to start analyzing your metagenome data
  ☆400Updated last month
• arpcard / rgi
  Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on h…
  ☆392Updated last month
• hyattpd / Prodigal
  Prodigal Gene Prediction Software
  ☆512Updated last year
• Ecogenomics / GTDBTk
  GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
  ☆548Updated last month
• amkozlov / raxml-ng
  RAxML Next Generation: faster, easier-to-use and more flexible
  ☆440Updated this week
• thackl / gggenomes
  A grammar of graphics for comparative genomics
  ☆699Updated 2 weeks ago
• mikolmogorov / Flye
  De novo assembler for single molecule sequencing reads using repeat graphs
  ☆878Updated 5 months ago
• s-andrews / FastQC
  A quality control analysis tool for high throughput sequencing data
  ☆544Updated last month
• ablab / spades
  SPAdes Genome Assembler
  ☆874Updated 2 weeks ago
• stamatak / standard-RAxML
  ☆346Updated 7 months ago