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.
  ☆128Updated last month
• rrwick / Autocycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆147Updated this week
• MDU-PHL / abritamr
  A pipeline for running AMRfinderPlus and collating results into functional classes
  ☆78Updated 10 months ago
• ncbi / fcs
  Foreign Contamination Screening caller scripts and documentation
  ☆130Updated 3 months ago
• bhattlab / MGEfinder
  A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
  ☆121Updated last year
• rrwick / Metagenomics-Index-Correction
  ☆82Updated last year
• nigyta / dfast_core
  DDBJ Fast Annotation and Submission Tool
  ☆79Updated last month
• xavierdidelot / ClonalFrameML
  ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
  ☆114Updated last year
• LomanLab / mockcommunity
  Long-read mock community experiments
  ☆105Updated 3 years ago
• gbouras13 / dnaapler
  Reorients assembled microbial sequences
  ☆121Updated 3 months ago
• artic-network / fieldbioinformatics
  The ARTIC field bioinformatics pipeline
  ☆124Updated 2 weeks ago
• xiezhq / ISEScan
  A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome
  ☆95Updated 2 months ago
• ncbi / SKESA
  SKESA assembler
  ☆119Updated 8 months ago
• CSB5 / OPERA-MS
  OPERA-MS - Hybrid Metagenomic Assembler
  ☆95Updated 11 months ago
• eead-csic-compbio / get_homologues
  GET_HOMOLOGUES: a versatile software package for pan-genome analysis
  ☆116Updated 3 months ago
• epi2me-labs / wf-metagenomics
  Metagenomic classification of long-read sequencing data
  ☆85Updated last month
• donovan-h-parks / CompareM
  A toolbox for comparative genomics.
  ☆104Updated 4 years ago
• medvedevgroup / SibeliaZ
  A fast whole-genome aligner based on de Bruijn graphs
  ☆150Updated 4 months ago
• lskatz / mashtree
  Create a tree using Mash distances
  ☆166Updated last year
• avierstr / amplicon_sorter
  Sorts amplicons from Nanopore sequencing data based on similarity
  ☆38Updated 3 weeks ago
• klebgenomics / Kleborate
  ☆125Updated last week
• bluenote-1577 / sylph
  ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.
  ☆231Updated 3 months ago
• wwood / singlem
  Novelty-inclusive microbial (and now dsDNA phage) community profiling of shotgun metagenomes
  ☆144Updated 2 weeks ago
• B-UMMI / chewBBACA
  BSR-Based Allele Calling Algorithm
  ☆147Updated this week
• rrwick / Polypolish
  a short-read polishing tool for long-read assemblies
  ☆170Updated last year
• thanhleviet / ISfinder-sequences
  Insertion sequences (Insertion Element) [https://en.wikipedia.org/wiki/Insertion_sequence] collected from ISfinder (https://isfinder.biot…
  ☆68Updated 4 years ago
• rrwick / Minipolish
  A tool for Racon polishing of miniasm assemblies
  ☆76Updated 3 weeks ago
• rrwick / Long-read-assembler-comparison
  Benchmarking of long-read assembly tools for bacterial whole genomes
  ☆171Updated 4 years ago
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆76Updated 3 years ago
• pierrebarbera / epa-ng
  Massively parallel phylogenetic placement of genetic sequences
  ☆84Updated 2 years ago