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 last month
• DerrickWood / kraken
  Kraken taxonomic sequence classification system
  ☆218Updated 4 years 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…
  ☆292Updated 2 months ago
• DaehwanKimLab / centrifuge
  Classifier for metagenomic sequences
  ☆267Updated 5 months ago
• najoshi / sickle
  Windowed Adaptive Trimming for fastq files using quality
  ☆226Updated 8 years ago
• neufeld / pandaseq
  PAired-eND Assembler for DNA sequences
  ☆137Updated 4 years ago
• fbreitwieser / pavian
  🌈 Interactive analysis of metagenomics data
  ☆436Updated 2 months ago
• cole-trapnell-lab / cufflinks
  ☆320Updated 5 years ago
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆243Updated 4 years ago
• ncbi / pgap
  NCBI Prokaryotic Genome Annotation Pipeline
  ☆362Updated last month
• marbl / Mash
  Fast genome and metagenome distance estimation using MinHash
  ☆428Updated 2 months ago
• TransDecoder / TransDecoder
  TransDecoder source
  ☆299Updated 2 months ago
• OpenGene / AfterQC
  Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
  ☆212Updated 5 years ago
• picrust / picrust
  Phylogenetic Investigation of Communities by Reconstruction of Unobserved STates (PICRUST): Official repository for software and unit tes…
  ☆91Updated 3 months ago
• stamatak / standard-RAxML
  ☆346Updated 9 months ago
• bioinformatics-centre / kaiju
  Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
  ☆295Updated 7 months 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
• timflutre / trimmomatic
  Read trimming tool for Illumina NGS data.
  ☆148Updated 10 years ago
• tseemann / barrnap
  Bacterial ribosomal RNA predictor
  ☆263Updated this week
• The-Sequence-Ontology / Specifications
  GFF and GVF specification documents
  ☆216Updated last year
• marbl / Krona
  Interactively explore metagenomes and more from a web browser.
  ☆491Updated 3 years ago
• nextgenusfs / funannotate
  Eukaryotic Genome Annotation Pipeline
  ☆369Updated 5 months ago
• sanger-pathogens / circlator
  A tool to circularize genome assemblies
  ☆249Updated last year
• biocore / emp
  Code repository of the Earth Microbiome Project.
  ☆163Updated 3 years ago
• Ecogenomics / CheckM
  Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
  ☆397Updated 6 months ago
• sortmerna / sortmerna
  SortMeRNA: next-generation sequence filtering and alignment tool
  ☆281Updated 3 months ago
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆372Updated 3 years ago
• arq5x / lumpy-sv
  lumpy: a general probabilistic framework for structural variant discovery
  ☆334Updated 3 years ago
• jts / sga
  de novo sequence assembler using string graphs
  ☆243Updated 6 years ago