Alternatives and similar repositories for parsnp

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

• gbouras13 / hybracter
  Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.
  ☆141Updated last month
• avierstr / amplicon_sorter
  Sorts amplicons from Nanopore sequencing data based on similarity
  ☆39Updated this week
• ncbi / fcs
  Foreign Contamination Screening caller scripts and documentation
  ☆139Updated 6 months ago
• nigyta / dfast_core
  DDBJ Fast Annotation and Submission Tool
  ☆83Updated last month
• xiezhq / ISEScan
  A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome
  ☆99Updated 6 months ago
• bhattlab / MGEfinder
  A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
  ☆123Updated last year
• LomanLab / mockcommunity
  Long-read mock community experiments
  ☆105Updated 4 years ago
• xavierdidelot / ClonalFrameML
  ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
  ☆116Updated last year
• thanhleviet / ISfinder-sequences
  Insertion sequences (Insertion Element) [https://en.wikipedia.org/wiki/Insertion_sequence] collected from ISfinder (https://isfinder.biot…
  ☆70Updated 5 years ago
• rrwick / Metagenomics-Index-Correction
  ☆84Updated 2 years ago
• gbouras13 / dnaapler
  Reorients assembled microbial sequences
  ☆128Updated last month
• ncbi / SKESA
  SKESA assembler
  ☆123Updated last year
• adlape95 / Assembly-methods-nanopore
  Assembly methods for nanopore-based metagenomic sequencing: a comparative study
  ☆18Updated 5 years ago
• MDU-PHL / abritamr
  A pipeline for running AMRfinderPlus and collating results into functional classes
  ☆81Updated last year
• CSB5 / OPERA-MS
  OPERA-MS - Hybrid Metagenomic Assembler
  ☆99Updated last year
• bonsai-team / Porechop_ABI
  Adapter trimmer for Oxford Nanopore reads using ab initio method
  ☆52Updated 10 months ago
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆69Updated 4 years ago
• KatariinaParnanen / MobileGeneticElementDatabase
  Contains a fasta format database of a large variety of mobile genetic elements and an annotation file
  ☆49Updated 4 years ago
• klebgenomics / Kleborate
  ☆129Updated 2 weeks ago
• donovan-h-parks / CompareM
  A toolbox for comparative genomics.
  ☆104Updated 4 years ago
• rrwick / Autocycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆190Updated 3 weeks ago
• patrickwest / EukRep
  Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets
  ☆75Updated last year
• qiyunlab / HGTector
  HGTector2: Genome-wide prediction of horizontal gene transfer based on distribution of sequence homology patterns.
  ☆135Updated 2 years ago
• BU-ISCIII / plasmidID
  PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identifi…
  ☆41Updated 4 years ago
• jhawkey / IS_mapper
  IS mapping software
  ☆56Updated 3 years ago
• shenwei356 / gtdb-taxdump
  GTDB taxonomy taxdump files with trackable TaxIds
  ☆55Updated 5 months ago
• fanglab / nanodisco
  nanodisco: a toolbox for discovering and exploiting multiple types of DNA methylation from individual bacteria and microbiomes using nano…
  ☆70Updated 3 years ago
• gem-pasteur / Integron_Finder
  Bioinformatics tool to find integrons in bacterial genomes
  ☆81Updated 5 months ago
• aineniamh / snipit
  snipit: summarise snps relative to your reference sequence
  ☆162Updated 3 weeks ago
• genomehubs / blobtoolkit
  Interactive quality assessment of genome assemblies
  ☆109Updated 5 months ago