Alternatives and similar repositories for parsnp

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

• nigyta / dfast_core
  DDBJ Fast Annotation and Submission Tool
  ☆83Updated 4 months ago
• gbouras13 / hybracter
  Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.
  ☆146Updated 2 weeks ago
• bhattlab / MGEfinder
  A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
  ☆124Updated 2 years ago
• rrwick / Metagenomics-Index-Correction
  ☆84Updated 2 years ago
• MDU-PHL / abritamr
  A pipeline for running AMRfinderPlus and collating results into functional classes
  ☆90Updated last month
• thanhleviet / ISfinder-sequences
  Insertion sequences (Insertion Element) [https://en.wikipedia.org/wiki/Insertion_sequence] collected from ISfinder (https://isfinder.biot…
  ☆73Updated 5 years ago
• xiezhq / ISEScan
  A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome
  ☆101Updated last month
• xavierdidelot / ClonalFrameML
  ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
  ☆119Updated last year
• ncbi / SKESA
  SKESA assembler
  ☆124Updated last year
• ncbi / fcs
  Foreign Contamination Screening caller scripts and documentation
  ☆156Updated 10 months ago
• nmquijada / tormes
  Making whole bacterial genome sequencing data analysis easy
  ☆114Updated 9 months ago
• medvedevgroup / SibeliaZ
  A fast whole-genome aligner based on de Bruijn graphs
  ☆157Updated 6 months ago
• CSB5 / OPERA-MS
  OPERA-MS - Hybrid Metagenomic Assembler
  ☆99Updated last year
• avierstr / amplicon_sorter
  Sorts amplicons from Nanopore sequencing data based on similarity
  ☆40Updated 3 months ago
• LomanLab / mockcommunity
  Long-read mock community experiments
  ☆104Updated 4 years ago
• qiyunlab / HGTector
  HGTector2: Genome-wide prediction of horizontal gene transfer based on distribution of sequence homology patterns.
  ☆143Updated 2 years ago
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆68Updated 4 years ago
• patrickwest / EukRep
  Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets
  ☆75Updated last year
• donovan-h-parks / CompareM
  A toolbox for comparative genomics.
  ☆108Updated 4 years ago
• gbouras13 / dnaapler
  Reorients assembled microbial sequences
  ☆131Updated 5 months ago
• gem-pasteur / Integron_Finder
  Bioinformatics tool to find integrons in bacterial genomes
  ☆83Updated 8 months ago
• bluenote-1577 / skani
  Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.
  ☆232Updated 3 months ago
• mjsull / Easyfig
  Development version of Easyfig
  ☆104Updated 2 years ago
• tseemann / snp-dists
  Pairwise SNP distance matrix from a FASTA sequence alignment
  ☆151Updated 3 weeks ago
• jhawkey / IS_mapper
  IS mapping software
  ☆57Updated 4 years ago
• fanglab / nanodisco
  nanodisco: a toolbox for discovering and exploiting multiple types of DNA methylation from individual bacteria and microbiomes using nano…
  ☆72Updated 3 years ago
• klebgenomics / Kleborate
  ☆135Updated 3 weeks ago
• wwood / singlem
  Novelty-inclusive microbial (and now dsDNA phage) community profiling of shotgun metagenomes
  ☆177Updated 2 weeks ago
• EBI-Metagenomics / emg-viral-pipeline
  VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
  ☆146Updated last month
• shenwei356 / gtdb-taxdump
  GTDB taxonomy taxdump files with trackable TaxIds
  ☆57Updated 8 months ago