Alternatives and similar repositories for aviary:

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

• takaram / kofam_scan
  CLI tool to annotate genes with KOfam
  ☆73Updated last year
• AnantharamanLab / vRhyme
  Binning Virus Genomes from Metagenomes
  ☆59Updated 2 years ago
• MDU-PHL / abritamr
  A pipeline for running AMRfinderPlus and collating results into functional classes
  ☆73Updated 5 months ago
• gem-pasteur / Integron_Finder
  Bioinformatics tool to find integrons in bacterial genomes
  ☆68Updated 7 months ago
• raw-lab / MetaCerberus
  Python code for versatile Functional Ontology Assignments for Metagenomes searching via Hidden Markov Model (HMM) with environmental focu…
  ☆53Updated last month
• moshi4 / ANIclustermap
  A tool for drawing ANI clustermap between all-vs-all microbial genomes
  ☆72Updated 4 months ago
• snayfach / MGV
  Supporting code for uncultivated gut virus manuscript
  ☆68Updated last year
• bhattlab / MGEfinder
  A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
  ☆114Updated last year
• gbouras13 / dnaapler
  Reorients assembled microbial sequences
  ☆107Updated 2 weeks ago
• Kalan-Lab / zol
  zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
  ☆52Updated last month
• rrwick / Autocycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆93Updated last week
• gbouras13 / hybracter
  Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.
  ☆113Updated last week
• gbouras13 / plassembler
  Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates
  ☆58Updated 2 weeks ago
• cultivarium / MicrobeMod
  A toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing
  ☆44Updated last week
• voorloopnul / awesome-phages
  A curated list of phage related software and computational resources for phage scientists, bioinformaticians and enthusiasts.
  ☆48Updated 2 years ago
• hzi-bifo / traitar
  From genomes to phenotypes: Traitar, the microbial trait analyzer
  ☆57Updated 5 years ago
• epi2me-labs / wf-bacterial-genomes
  Small variant calling for haploid samples
  ☆29Updated 3 weeks ago
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆69Updated 3 years ago
• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆70Updated last year
• bvalot / pyMLST
  whole genome MLST analysis
  ☆40Updated 8 months ago
• endixk / ezaai
  EzAAI - High Throughput Prokaryotic AAI Calculator
  ☆37Updated 3 months ago
• HRGV / phyloFlash
  phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
  ☆81Updated last year
• SionBayliss / PIRATE
  A toolbox for pangenome analysis and threshold evaluation.
  ☆92Updated 2 years ago
• BigDataBiology / argNorm
  ARG normalization by mapping to the ARO ontology.
  ☆29Updated this week
• soedinglab / spacepharer
  SpacePHARER CRISPR Spacer Phage-Host pAiRs findER
  ☆37Updated 8 months ago
• GaetanBenoitDev / metaMDBG
  MetaMDBG: a lightweight assembler for long and accurate metagenomics reads.
  ☆132Updated last month
• bluenote-1577 / skani
  Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.
  ☆180Updated 6 months ago
• bhattlab / phanta
  Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes
  ☆61Updated last month
• oschwengers / asap
  A scalable bacterial genome assembly, annotation and analysis pipeline
  ☆71Updated last year
• jhawkey / IS_mapper
  IS mapping software
  ☆53Updated 3 years ago