Alternatives and similar repositories for qiime

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

• ncbi / pgap
  NCBI Prokaryotic Genome Annotation Pipeline
  ☆339Updated 2 weeks ago
• Ecogenomics / CheckM
  Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
  ☆376Updated 2 weeks ago
• arq5x / poretools
  a toolkit for working with Oxford nanopore data
  ☆243Updated 2 years ago
• DaehwanKimLab / centrifuge
  Classifier for metagenomic sequences
  ☆260Updated last week
• ablab / quast
  Genome assembly evaluation tool
  ☆441Updated 7 months ago
• mothur / mothur
  Welcome to the mothur project, initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology & Imm…
  ☆272Updated last month
• sanger-pathogens / Roary
  Rapid large-scale prokaryote pan genome analysis
  ☆351Updated 3 years ago
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆367Updated 3 years ago
• bxlab / metaWRAP
  MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
  ☆426Updated last year
• stamatak / standard-RAxML
  ☆341Updated 3 months ago
• nextgenusfs / funannotate
  Eukaryotic Genome Annotation Pipeline
  ☆355Updated last month
• fbreitwieser / pavian
  🌈 Interactive analysis of metagenomics data
  ☆421Updated 9 months ago
• rrwick / Trycycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆324Updated last year
• jenniferlu717 / Bracken
  Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species i…
  ☆310Updated 4 months ago
• tseemann / barrnap
  Bacterial ribosomal RNA predictor
  ☆246Updated last year
• tseemann / shovill
  ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads
  ☆229Updated 2 years ago
• rrwick / Unicycler
  hybrid assembly pipeline for bacterial genomes
  ☆601Updated 11 months ago
• jenniferlu717 / KrakenTools
  KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
  ☆343Updated last year
• jtamames / SqueezeMeta
  A complete pipeline for metagenomic analysis
  ☆417Updated last week
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆234Updated 4 years ago
• oschwengers / bakta
  Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
  ☆530Updated this week
• mmatschiner / tutorials
  Tutorials on phylogenetic and phylogenomic inference
  ☆386Updated last year
• ndierckx / NOVOPlasty
  NOVOPlasty - The organelle assembler and heteroplasmy caller
  ☆188Updated last year
• qiime2 / qiime2
  Source for the QIIME 2 Framework (Q2F).
  ☆505Updated 2 weeks ago
• bioinformatics-centre / kaiju
  Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
  ☆282Updated 2 months ago
• sanger-pathogens / circlator
  A tool to circularize genome assemblies
  ☆242Updated last year
• AstrobioMike / GToTree
  A user-friendly workflow for phylogenomics
  ☆213Updated 2 weeks ago
• nf-core / ampliseq
  Amplicon sequencing analysis workflow using DADA2 and QIIME2
  ☆207Updated last week
• edgardomortiz / vcf2phylip
  Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
  ☆312Updated last year
• picrust / picrust2
  Code, unit tests, and tutorials for running PICRUSt2
  ☆361Updated 2 months ago