Alternatives and similar repositories for aviary:

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

• HRGV / phyloFlash
  phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
  ☆83Updated last year
• gem-pasteur / Integron_Finder
  Bioinformatics tool to find integrons in bacterial genomes
  ☆71Updated 9 months ago
• gbouras13 / dnaapler
  Reorients assembled microbial sequences
  ☆116Updated last week
• gbouras13 / hybracter
  Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.
  ☆122Updated 3 weeks ago
• SionBayliss / PIRATE
  A toolbox for pangenome analysis and threshold evaluation.
  ☆94Updated 2 years ago
• donovan-h-parks / CompareM
  A toolbox for comparative genomics.
  ☆101Updated 3 years ago
• bluenote-1577 / skani
  Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.
  ☆191Updated 8 months ago
• snayfach / MGV
  Supporting code for uncultivated gut virus manuscript
  ☆69Updated last year
• takaram / kofam_scan
  CLI tool to annotate genes with KOfam
  ☆78Updated last year
• AnantharamanLab / vRhyme
  Binning Virus Genomes from Metagenomes
  ☆62Updated 2 years ago
• bhattlab / MGEfinder
  A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
  ☆116Updated last year
• moshi4 / COGclassifier
  A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category
  ☆62Updated 6 months ago
• Kalan-Lab / zol
  zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
  ☆58Updated last month
• Carrion-lab / bacLIFE
  ☆44Updated last month
• moshi4 / ANIclustermap
  A tool for drawing ANI clustermap between all-vs-all microbial genomes
  ☆75Updated 6 months ago
• MDU-PHL / abritamr
  A pipeline for running AMRfinderPlus and collating results into functional classes
  ☆75Updated 7 months ago
• aleimba / bac-genomics-scripts
  Collection of scripts for bacterial genomics
  ☆45Updated 5 years ago
• xavierdidelot / ClonalFrameML
  ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
  ☆114Updated 10 months ago
• rrwick / Polypolish
  a short-read polishing tool for long-read assemblies
  ☆156Updated 9 months ago
• CDCgov / mycosnp-nf
  CDCgov/mycosnp-nf
  ☆49Updated this week
• raw-lab / MetaCerberus
  Python code for versatile Functional Ontology Assignments for Metagenomes searching via Hidden Markov Model (HMM) with environmental focu…
  ☆55Updated last month
• GaetanBenoitDev / metaMDBG
  MetaMDBG: a lightweight assembler for long and accurate metagenomics reads.
  ☆141Updated 4 months ago
• patrickwest / EukRep
  Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets
  ☆69Updated 9 months ago
• ablab / viralVerify
  viralVerify: viral contig verification tool
  ☆67Updated 3 years ago
• bede / hostile
  Precise host read removal
  ☆92Updated 3 months ago
• lskatz / mashtree
  Create a tree using Mash distances
  ☆160Updated last year
• nigyta / dfast_core
  DDBJ Fast Annotation and Submission Tool
  ☆79Updated last month
• rrwick / Autocycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆113Updated this week
• vrmarcelino / CCMetagen
  Microbiome classification pipeline
  ☆66Updated last week
• hzi-bifo / traitar
  From genomes to phenotypes: Traitar, the microbial trait analyzer
  ☆57Updated 5 years ago