Alternatives and similar repositories for prokka:

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

• mikolmogorov / Flye
  De novo assembler for single molecule sequencing reads using repeat graphs
  ☆826Updated last week
• eggnogdb / eggnog-mapper
  Fast genome-wide functional annotation through orthology assignment
  ☆616Updated 11 months ago
• davidemms / OrthoFinder
  Phylogenetic orthology inference for comparative genomics
  ☆755Updated 6 months ago
• oschwengers / bakta
  Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
  ☆506Updated last month
• DerrickWood / kraken2
  The second version of the Kraken taxonomic sequence classification system
  ☆784Updated 2 weeks ago
• rrwick / Unicycler
  hybrid assembly pipeline for bacterial genomes
  ☆596Updated 9 months ago
• tseemann / snippy
  Rapid haploid variant calling and core genome alignment
  ☆511Updated 9 months ago
• bxlab / metaWRAP
  MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
  ☆419Updated last year
• sanger-pathogens / Roary
  Rapid large-scale prokaryote pan genome analysis
  ☆344Updated 3 years ago
• ablab / spades
  SPAdes Genome Assembler
  ☆819Updated this week
• tseemann / abricate
  Mass screening of contigs for antimicrobial and virulence genes
  ☆410Updated last year
• hyattpd / Prodigal
  Prodigal Gene Prediction Software
  ☆484Updated last year
• gamcil / clinker
  Gene cluster comparison figure generator
  ☆572Updated 5 months ago
• ablab / quast
  Genome assembly evaluation tool
  ☆431Updated 5 months ago
• jtamames / SqueezeMeta
  A complete pipeline for metagenomic analysis
  ☆406Updated last week
• Ecogenomics / CheckM
  Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
  ☆371Updated 8 months ago
• tanghaibao / jcvi
  Python library to facilitate genome assembly, annotation, and comparative genomics
  ☆817Updated 2 weeks ago
• nanoporetech / medaka
  Sequence correction provided by ONT Research
  ☆452Updated 6 months ago
• chhylp123 / hifiasm
  Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
  ☆614Updated last month
• biobakery / MetaPhlAn
  MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
  ☆339Updated 2 weeks ago
• metagenome-atlas / atlas
  ATLAS - Three commands to start analyzing your metagenome data
  ☆387Updated last month
• bwa-mem2 / bwa-mem2
  The next version of bwa-mem
  ☆751Updated 9 months ago
• arpcard / rgi
  Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on h…
  ☆362Updated last week
• marbl / canu
  A single molecule sequence assembler for genomes large and small.
  ☆674Updated 2 weeks ago
• ncbi / pgap
  NCBI Prokaryotic Genome Annotation Pipeline
  ☆335Updated last week
• rrwick / Bandage
  a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
  ☆612Updated 2 years ago
• wdecoster / NanoPlot
  Plotting scripts for long read sequencing data
  ☆473Updated 3 months ago
• jorvis / biocode
  Bioinformatics code libraries and scripts
  ☆523Updated 2 months ago
• jenniferlu717 / KrakenTools
  KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
  ☆338Updated last year
• bactopia / bactopia
  A flexible pipeline for complete analysis of bacterial genomes
  ☆456Updated last week