Alternatives and similar repositories for PIRATE:

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

• gbouras13 / hybracter
  Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.
  ☆126Updated last month
• MDU-PHL / abritamr
  A pipeline for running AMRfinderPlus and collating results into functional classes
  ☆77Updated 8 months ago
• oschwengers / asap
  A scalable bacterial genome assembly, annotation and analysis pipeline
  ☆73Updated last year
• xavierdidelot / ClonalFrameML
  ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
  ☆114Updated 11 months ago
• bhattlab / MGEfinder
  A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
  ☆117Updated last year
• rrwick / Polypolish
  a short-read polishing tool for long-read assemblies
  ☆158Updated 10 months ago
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆76Updated 3 years ago
• HRGV / phyloFlash
  phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
  ☆85Updated last year
• ncbi / SKESA
  SKESA assembler
  ☆116Updated 6 months ago
• gbouras13 / dnaapler
  Reorients assembled microbial sequences
  ☆116Updated last month
• epi2me-labs / wf-metagenomics
  Metagenomic classification of long-read sequencing data
  ☆81Updated 3 weeks ago
• ncbi / fcs
  Foreign Contamination Screening caller scripts and documentation
  ☆129Updated last month
• rrwick / Autocycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆125Updated last week
• nmquijada / tormes
  Making whole bacterial genome sequencing data analysis easy
  ☆106Updated 2 weeks ago
• nigyta / dfast_core
  DDBJ Fast Annotation and Submission Tool
  ☆80Updated this week
• jhawkey / IS_mapper
  IS mapping software
  ☆54Updated 3 years ago
• bjtully / BioData
  All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")
  ☆73Updated 2 years ago
• donovan-h-parks / CompareM
  A toolbox for comparative genomics.
  ☆103Updated 3 years ago
• snayfach / MGV
  Supporting code for uncultivated gut virus manuscript
  ☆71Updated 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
• bacpop / PopPUNK
  PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
  ☆97Updated last month
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆70Updated 3 years ago
• gtonkinhill / panstripe
  post processing of bacterial pangenome gene presence/absence matrices
  ☆60Updated 2 months ago
• filip-husnik / pseudofinder
  Detection of pseudogene candidates in bacterial and archaeal genomes.
  ☆49Updated last year
• fwhelan / coinfinder
  A tool for the identification of coincident (associating and dissociating) genes in pangenomes.
  ☆101Updated last year
• lskatz / mashtree
  Create a tree using Mash distances
  ☆163Updated last year
• avierstr / amplicon_sorter
  Sorts amplicons from Nanopore sequencing data based on similarity
  ☆37Updated last month
• genomehubs / blobtoolkit
  Interactive quality assessment of genome assemblies
  ☆99Updated last month
• patrickwest / EukRep
  Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets
  ☆69Updated 10 months ago
• hzi-bifo / traitar
  From genomes to phenotypes: Traitar, the microbial trait analyzer
  ☆59Updated 5 years ago