Alternatives and similar repositories for PIRATE:

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

• xavierdidelot / ClonalFrameML
  ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
  ☆112Updated 8 months ago
• HRGV / phyloFlash
  phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
  ☆81Updated last year
• eead-csic-compbio / get_homologues
  GET_HOMOLOGUES: a versatile software package for pan-genome analysis
  ☆111Updated last month
• gbouras13 / hybracter
  Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.
  ☆115Updated 2 weeks ago
• oschwengers / asap
  A scalable bacterial genome assembly, annotation and analysis pipeline
  ☆72Updated last year
• bhattlab / MGEfinder
  A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
  ☆115Updated last year
• rrwick / Polypolish
  a short-read polishing tool for long-read assemblies
  ☆153Updated 8 months ago
• MaestSi / MetONTIIME
  A Meta-barcoding pipeline for analysing ONT data in QIIME2 framework
  ☆91Updated 8 months ago
• lskatz / mashtree
  Create a tree using Mash distances
  ☆157Updated last year
• nmquijada / tormes
  Making whole bacterial genome sequencing data analysis easy
  ☆103Updated 3 months ago
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆76Updated 2 years ago
• bjtully / BioData
  All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")
  ☆71Updated last year
• nigyta / dfast_core
  DDBJ Fast Annotation and Submission Tool
  ☆78Updated last week
• gbouras13 / dnaapler
  Reorients assembled microbial sequences
  ☆109Updated this week
• MDU-PHL / abritamr
  A pipeline for running AMRfinderPlus and collating results into functional classes
  ☆73Updated 5 months ago
• epi2me-labs / wf-metagenomics
  Metagenomic classification of long-read sequencing data
  ☆74Updated this week
• rrwick / Autocycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆97Updated 3 weeks ago
• ncbi / fcs
  Foreign Contamination Screening caller scripts and documentation
  ☆122Updated 2 months ago
• patrickwest / EukRep
  Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets
  ☆69Updated 7 months ago
• transcript / samsa2
  SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…
  ☆57Updated 10 months ago
• donovan-h-parks / CompareM
  A toolbox for comparative genomics.
  ☆101Updated 3 years ago
• cmks / DAS_Tool
  DAS Tool
  ☆146Updated 9 months ago
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆69Updated 3 years ago
• wwood / singlem
  Novelty-inclusive microbial community profiling of shotgun metagenomes
  ☆138Updated last week
• jhawkey / IS_mapper
  IS mapping software
  ☆53Updated 3 years ago
• RemiAllio / MitoFinder
  MitoFinder: efficient automated large-scale extraction of mitogenomic data from high throughput sequencing data
  ☆96Updated 10 months ago
• MrOlm / inStrain
  Bioinformatics program inStrain
  ☆159Updated 9 months ago
• rrwick / Metagenomics-Index-Correction
  ☆79Updated last year
• snayfach / MGV
  Supporting code for uncultivated gut virus manuscript
  ☆68Updated last year
• gem-pasteur / Integron_Finder
  Bioinformatics tool to find integrons in bacterial genomes
  ☆69Updated 8 months ago