Alternatives and similar repositories for ncbi-genome-download

Users that are interested in ncbi-genome-download are comparing it to the libraries listed below

• oschwengers / bakta

  View on GitHub
  Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
  ☆606Feb 9, 2026Updated last week
• ParBLiSS / FastANI

  View on GitHub
  Fast Whole-Genome Similarity (ANI) Estimation
  ☆447Dec 16, 2025Updated 2 months ago
• rrwick / Unicycler

  View on GitHub
  hybrid assembly pipeline for bacterial genomes
  ☆632Jul 25, 2024Updated last year
• kblin / ncbi-acc-download

  View on GitHub
  Download files from NCBI Entrez by accession
  ☆134Sep 3, 2024Updated last year
• Ecogenomics / GTDBTk

  View on GitHub
  GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
  ☆574Feb 9, 2026Updated last week
• tseemann / abricate

  View on GitHub
  Mass screening of contigs for antimicrobial and virulence genes
  ☆479Jan 31, 2026Updated 2 weeks ago
• bactopia / bactopia

  View on GitHub
  A flexible pipeline for complete analysis of bacterial genomes
  ☆499Dec 19, 2025Updated last month
• shenwei356 / taxonkit

  View on GitHub
  A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
  ☆457Updated this week
• MrOlm / drep

  View on GitHub
  Rapid comparison and dereplication of genomes
  ☆326Nov 10, 2025Updated 3 months ago
• tseemann / prokka

  View on GitHub
  Rapid prokaryotic genome annotation
  ☆957Jan 6, 2026Updated last month
• gtonkinhill / panaroo

  View on GitHub
  An updated pipeline for pangenome investigation
  ☆341Jan 15, 2026Updated last month
• tseemann / snippy

  View on GitHub
  Rapid haploid variant calling and core genome alignment
  ☆565Dec 12, 2025Updated 2 months ago
• rrwick / Trycycler

  View on GitHub
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆339Sep 11, 2025Updated 5 months ago
• sourmash-bio / sourmash

  View on GitHub
  Quickly search, compare, and analyze genomic and metagenomic data sets.
  ☆538Feb 9, 2026Updated last week
• eggnogdb / eggnog-mapper

  View on GitHub
  Fast genome-wide functional annotation through orthology assignment
  ☆700Jun 18, 2025Updated 7 months ago
• tseemann / shovill

  View on GitHub
  ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads
  ☆254Dec 13, 2025Updated 2 months ago
• OpenGene / fastp

  View on GitHub
  An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
  ☆2,283Jan 22, 2026Updated 3 weeks ago
• gamcil / clinker

  View on GitHub
  Gene cluster comparison figure generator
  ☆635Dec 22, 2025Updated last month
• bxlab / metaWRAP

  View on GitHub
  MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
  ☆459Jul 28, 2023Updated 2 years ago
• shenwei356 / seqkit

  View on GitHub
  A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
  ☆1,510Feb 9, 2026Updated last week
• jenniferlu717 / KrakenTools

  View on GitHub
  KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
  ☆366Aug 1, 2025Updated 6 months ago
• widdowquinn / pyani

  View on GitHub
  Application and Python module for average nucleotide identity analyses of microbes.
  ☆217Jul 1, 2025Updated 7 months ago
• Ecogenomics / CheckM

  View on GitHub
  Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
  ☆401Jun 12, 2025Updated 8 months ago
• sanger-pathogens / Roary

  View on GitHub
  Rapid large-scale prokaryote pan genome analysis
  ☆371Nov 3, 2025Updated 3 months ago
• merenlab / anvio

  View on GitHub
  An analysis and visualization platform for 'omics data
  ☆504Updated this week
• metagenome-atlas / atlas

  View on GitHub
  ATLAS - Three commands to start analyzing your metagenome data
  ☆402Nov 28, 2025Updated 2 months ago
• WrightonLabCSU / DRAM

  View on GitHub
  Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
  ☆319Feb 3, 2026Updated 2 weeks ago
• AstrobioMike / GToTree

  View on GitHub
  A user-friendly workflow for phylogenomics
  ☆225Feb 5, 2026Updated last week
• bbuchfink / diamond

  View on GitHub
  Accelerated BLAST compatible local sequence aligner.
  ☆1,239Feb 7, 2026Updated last week
• arpcard / rgi

  View on GitHub
  Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on h…
  ☆403Jan 12, 2026Updated last month
• labgem / PPanGGOLiN

  View on GitHub
  Build a partitioned pangenome graph from microbial genomes
  ☆293Dec 17, 2025Updated 2 months ago
• sanger-pathogens / circlator

  View on GitHub
  A tool to circularize genome assemblies
  ☆252Apr 6, 2024Updated last year
• ncbi / amr

  View on GitHub
  AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and p…
  ☆350Jan 31, 2026Updated 2 weeks ago
• CAMI-challenge / CAMISIM

  View on GitHub
  CAMISIM: Simulating metagenomes and microbial communities
  ☆221Feb 10, 2026Updated last week
• marbl / Mash

  View on GitHub
  Fast genome and metagenome distance estimation using MinHash
  ☆434Sep 19, 2025Updated 4 months ago
• wwood / CoverM

  View on GitHub
  Read alignment statistics for metagenomics
  ☆387Jan 16, 2026Updated last month
• AdmiralenOla / Scoary

  View on GitHub
  Pan-genome wide association studies
  ☆207May 29, 2024Updated last year
• bioinformatics-centre / kaiju

  View on GitHub
  Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
  ☆298Apr 25, 2025Updated 9 months ago
• lskatz / mashtree

  View on GitHub
  Create a tree using Mash distances
  ☆182Oct 24, 2023Updated 2 years ago