Alternatives and similar repositories for snippy

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

• rrwick / Porechop
  adapter trimmer for Oxford Nanopore reads
  ☆371Updated last year
• wdecoster / NanoPlot
  Plotting scripts for long read sequencing data
  ☆498Updated 2 weeks ago
• ablab / quast
  Genome assembly evaluation tool
  ☆464Updated 10 months ago
• oschwengers / bakta
  Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
  ☆549Updated 2 weeks ago
• rrwick / Unicycler
  hybrid assembly pipeline for bacterial genomes
  ☆612Updated last year
• Gaius-Augustus / BRAKER
  BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eu…
  ☆423Updated 7 months ago
• malonge / RagTag
  Tools for fast and flexible genome assembly scaffolding and improvement
  ☆528Updated last year
• nanoporetech / medaka
  Sequence correction provided by ONT Research
  ☆480Updated 3 weeks ago
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆368Updated 3 years ago
• nextgenusfs / funannotate
  Eukaryotic Genome Annotation Pipeline
  ☆362Updated 2 months ago
• tseemann / abricate
  Mass screening of contigs for antimicrobial and virulence genes
  ☆434Updated last year
• bxlab / metaWRAP
  MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
  ☆441Updated 2 years ago
• sanger-pathogens / Roary
  Rapid large-scale prokaryote pan genome analysis
  ☆354Updated 3 years ago
• jenniferlu717 / KrakenTools
  KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
  ☆349Updated last month
• Ecogenomics / CheckM
  Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
  ☆384Updated 3 months ago
• mikolmogorov / Flye
  De novo assembler for single molecule sequencing reads using repeat graphs
  ☆868Updated 4 months ago
• rrwick / Filtlong
  quality filtering tool for long reads
  ☆365Updated last month
• jtamames / SqueezeMeta
  A complete pipeline for metagenomic analysis
  ☆427Updated 2 weeks ago
• mummer4 / mummer
  Mummer alignment tool
  ☆524Updated 7 months ago
• ncbi / pgap
  NCBI Prokaryotic Genome Annotation Pipeline
  ☆354Updated 2 weeks ago
• bactopia / bactopia
  A flexible pipeline for complete analysis of bacterial genomes
  ☆472Updated this week
• arpcard / rgi
  Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on h…
  ☆384Updated this week
• fbreitwieser / pavian
  🌈 Interactive analysis of metagenomics data
  ☆423Updated last month
• rrwick / Trycycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆332Updated last week
• biobakery / MetaPhlAn
  MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
  ☆364Updated last week
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆239Updated 4 years ago
• shenwei356 / taxonkit
  A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
  ☆434Updated 4 months ago
• ParBLiSS / FastANI
  Fast Whole-Genome Similarity (ANI) Estimation
  ☆427Updated last month
• gamcil / clinker
  Gene cluster comparison figure generator
  ☆608Updated 9 months ago
• usadellab / Trimmomatic
  ☆266Updated 3 weeks ago