Alternatives and similar repositories for snippy:

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

• tseemann / abricate
  Mass screening of contigs for antimicrobial and virulence genes
  ☆401Updated last year
• jenniferlu717 / KrakenTools
  KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
  ☆333Updated last year
• oschwengers / bakta
  Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
  ☆497Updated last month
• malonge / RagTag
  Tools for fast and flexible genome assembly scaffolding and improvement
  ☆500Updated last year
• rrwick / Trycycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆318Updated 10 months ago
• sanger-pathogens / Roary
  Rapid large-scale prokaryote pan genome analysis
  ☆341Updated 2 years ago
• rrwick / Unicycler
  hybrid assembly pipeline for bacterial genomes
  ☆592Updated 8 months ago
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆357Updated 3 years ago
• nanoporetech / medaka
  Sequence correction provided by ONT Research
  ☆449Updated 6 months ago
• 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…
  ☆394Updated 2 months ago
• nextgenusfs / funannotate
  Eukaryotic Genome Annotation Pipeline
  ☆345Updated last month
• bxlab / metaWRAP
  MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
  ☆419Updated last year
• tseemann / mlst
  Scan contig files against PubMLST typing schemes
  ☆221Updated 2 years ago
• Ecogenomics / CheckM
  Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
  ☆367Updated 7 months ago
• rrwick / Porechop
  adapter trimmer for Oxford Nanopore reads
  ☆356Updated 11 months ago
• ncbi / pgap
  NCBI Prokaryotic Genome Annotation Pipeline
  ☆332Updated this week
• bactopia / bactopia
  A flexible pipeline for complete analysis of bacterial genomes
  ☆452Updated last week
• rrwick / Filtlong
  quality filtering tool for long reads
  ☆326Updated last year
• wdecoster / NanoPlot
  Plotting scripts for long read sequencing data
  ☆467Updated 2 months ago
• arpcard / rgi
  Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on h…
  ☆359Updated this week
• sanger-pathogens / snp-sites
  Finds SNP sites from a multi-FASTA alignment file
  ☆257Updated 4 years ago
• biobakery / MetaPhlAn
  MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
  ☆335Updated last week
• TransDecoder / TransDecoder
  TransDecoder source
  ☆288Updated 6 months ago
• jtamames / SqueezeMeta
  A complete pipeline for metagenomic analysis
  ☆400Updated this week
• jenniferlu717 / Bracken
  Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species i…
  ☆305Updated last month
• eggnogdb / eggnog-mapper
  Fast genome-wide functional annotation through orthology assignment
  ☆608Updated 11 months ago
• mikolmogorov / Flye
  De novo assembler for single molecule sequencing reads using repeat graphs
  ☆820Updated 7 months ago
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆226Updated 4 years ago
• mummer4 / mummer
  Mummer alignment tool
  ☆495Updated 2 months ago
• usadellab / Trimmomatic
  ☆242Updated 10 months ago