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
  ☆79Updated last year
• donovan-h-parks / CompareM
  A toolbox for comparative genomics.
  ☆103Updated 3 years ago
• gbouras13 / dnaapler
  Reorients assembled microbial sequences
  ☆116Updated last month
• HRGV / phyloFlash
  phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
  ☆85Updated last year
• snayfach / MGV
  Supporting code for uncultivated gut virus manuscript
  ☆71Updated last year
• AnantharamanLab / vRhyme
  Binning Virus Genomes from Metagenomes
  ☆62Updated 2 years ago
• moshi4 / ANIclustermap
  A tool for drawing ANI clustermap between all-vs-all microbial genomes
  ☆76Updated 7 months ago
• MDU-PHL / abritamr
  A pipeline for running AMRfinderPlus and collating results into functional classes
  ☆76Updated 8 months ago
• gem-pasteur / Integron_Finder
  Bioinformatics tool to find integrons in bacterial genomes
  ☆72Updated 10 months ago
• patrickwest / EukRep
  Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets
  ☆69Updated 10 months ago
• ablab / viralVerify
  viralVerify: viral contig verification tool
  ☆68Updated 3 years ago
• gbouras13 / hybracter
  Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.
  ☆126Updated last month
• SionBayliss / PIRATE
  A toolbox for pangenome analysis and threshold evaluation.
  ☆96Updated 2 years ago
• bhattlab / MGEfinder
  A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
  ☆117Updated last year
• BigDataBiology / argNorm
  ARG normalization by mapping to the ARO ontology.
  ☆47Updated this week
• nigyta / dfast_core
  DDBJ Fast Annotation and Submission Tool
  ☆80Updated 2 months ago
• Hydro3639 / NanoPhase
  Reference-quality genome reconstruction from complex metagenomes (or bacterial isolates) using only Nanopore long reads or both long and …
  ☆32Updated last year
• aleimba / bac-genomics-scripts
  Collection of scripts for bacterial genomics
  ☆45Updated 5 years ago
• raw-lab / MetaCerberus
  Python code for versatile Functional Ontology Assignments for Metagenomes searching via Hidden Markov Model (HMM) with environmental focu…
  ☆57Updated last week
• Kalan-Lab / zol
  zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
  ☆59Updated last week
• moshi4 / COGclassifier
  A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category
  ☆62Updated last week
• EBI-Metagenomics / mobilome-annotation-pipeline
  ☆43Updated last week
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆70Updated 3 years ago
• gbouras13 / plassembler
  Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates
  ☆61Updated 3 months ago
• allind / EukDetect
  ☆50Updated last year
• bluenote-1577 / skani
  Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.
  ☆196Updated 9 months ago
• Carrion-lab / bacLIFE
  ☆44Updated 2 months ago
• jolespin / veba
  A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metag…
  ☆83Updated last week
• linxingchen / cobra
  A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during…
  ☆70Updated 8 months ago
• mdsufz / MuDoGeR
  MuDoGeR makes the recovery of genomes from prokaryotes, viruses, and eukaryotes from metagenomes easy.
  ☆88Updated 8 months ago