Alternatives and similar repositories for qiime

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

• mothur / mothur
  Welcome to the mothur project, initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology & Imm…
  ☆274Updated this week
• DerrickWood / kraken
  Kraken taxonomic sequence classification system
  ☆217Updated 4 years ago
• stamatak / standard-RAxML
  ☆346Updated 8 months ago
• DaehwanKimLab / centrifuge
  Classifier for metagenomic sequences
  ☆266Updated 4 months ago
• arq5x / poretools
  a toolkit for working with Oxford nanopore data
  ☆245Updated 2 years ago
• dzerbino / velvet
  Short read de novo assembler using de Bruijn graphs, as published in: D.R. Zerbino and E. Birney. 2008. Velvet: algorithms for de novo sh…
  ☆293Updated 3 weeks ago
• fbreitwieser / pavian
  🌈 Interactive analysis of metagenomics data
  ☆429Updated last month
• marbl / Mash
  Fast genome and metagenome distance estimation using MinHash
  ☆424Updated last month
• najoshi / sickle
  Windowed Adaptive Trimming for fastq files using quality
  ☆226Updated 8 years ago
• broadinstitute / viral-ngs
  [THIS REPO IS DEPRECATED] see newer repos: https://github.com/broadinstitute/viral-core https://github.com/broadinstitute/viral-assemble …
  ☆195Updated last year
• picrust / picrust
  Phylogenetic Investigation of Communities by Reconstruction of Unobserved STates (PICRUST): Official repository for software and unit tes…
  ☆91Updated 2 months ago
• bioinformatics-centre / kaiju
  Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
  ☆295Updated 6 months ago
• ncbi / pgap
  NCBI Prokaryotic Genome Annotation Pipeline
  ☆358Updated 3 weeks ago
• OpenGene / AfterQC
  Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
  ☆212Updated 5 years ago
• cole-trapnell-lab / cufflinks
  ☆319Updated 5 years ago
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆242Updated 4 years ago
• neufeld / pandaseq
  PAired-eND Assembler for DNA sequences
  ☆137Updated 4 years ago
• jenniferlu717 / Bracken
  Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species i…
  ☆322Updated 8 months ago
• sanger-pathogens / circlator
  A tool to circularize genome assemblies
  ☆248Updated last year
• marbl / Krona
  Interactively explore metagenomes and more from a web browser.
  ☆491Updated 3 years ago
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆370Updated 3 years ago
• sanger-pathogens / Roary
  Rapid large-scale prokaryote pan genome analysis
  ☆355Updated last week
• qiime2 / qiime2
  Source for the QIIME 2 Framework (Q2F).
  ☆520Updated last week
• ablab / quast
  Genome assembly evaluation tool
  ☆474Updated 11 months ago
• Ecogenomics / CheckM
  Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
  ☆392Updated 4 months ago
• sanger-pathogens / Artemis
  Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the…
  ☆258Updated last year
• timflutre / trimmomatic
  Read trimming tool for Illumina NGS data.
  ☆146Updated 10 years ago
• biocore / emp
  Code repository of the Earth Microbiome Project.
  ☆163Updated 2 years ago
• jtamames / SqueezeMeta
  A complete pipeline for metagenomic analysis
  ☆437Updated last week
• nextgenusfs / funannotate
  Eukaryotic Genome Annotation Pipeline
  ☆366Updated 4 months ago