Alternatives and similar repositories for plasmidID

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

• aldertzomer / RFPlasmid
  Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf
  ☆49Updated last year
• nekokoe / Plasmer
  An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features.
  ☆48Updated 2 years ago
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆69Updated 4 years ago
• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆77Updated last month
• gtonkinhill / panstripe
  post processing of bacterial pangenome gene presence/absence matrices
  ☆61Updated 7 months ago
• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆35Updated 4 years ago
• linsalrob / PhiSpy
  Prediction of prophages from bacterial genomes
  ☆81Updated 3 months ago
• MDU-PHL / abritamr
  A pipeline for running AMRfinderPlus and collating results into functional classes
  ☆81Updated last year
• adlape95 / Assembly-methods-nanopore
  Assembly methods for nanopore-based metagenomic sequencing: a comparative study
  ☆18Updated 5 years ago
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆77Updated 3 years ago
• avierstr / amplicon_sorter
  Sorts amplicons from Nanopore sequencing data based on similarity
  ☆39Updated 4 months ago
• jhawkey / IS_mapper
  IS mapping software
  ☆56Updated 3 years ago
• Serka-M / mmlong2
  Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes
  ☆51Updated this week
• gem-pasteur / PanACoTA
  PANgenome with Annotations, COre identification, Tree and corresponding Alignments
  ☆74Updated 2 years ago
• thanhleviet / ISfinder-sequences
  Insertion sequences (Insertion Element) [https://en.wikipedia.org/wiki/Insertion_sequence] collected from ISfinder (https://isfinder.biot…
  ☆70Updated 5 years ago
• songweizhi / MetaCHIP
  Horizontal gene transfer (HGT) identification pipeline
  ☆63Updated 2 years ago
• shenwei356 / gtdb-taxdump
  GTDB taxonomy taxdump files with trackable TaxIds
  ☆55Updated 5 months ago
• patrickwest / EukRep_Pipeline
  ☆24Updated 6 years ago
• phac-nml / sistr_cmd
  SISTR (Salmonella In Silico Typing Resource) command-line tool
  ☆31Updated 5 months ago
• tseemann / phastaf
  Identify phage regions in bacterial genomes for masking purposes
  ☆34Updated 6 years ago
• egonozer / in_silico_pcr
  Perl script for simulating PCR reactions. Extract sequences from a query based on primer sequences.
  ☆47Updated 6 months ago
• bvalot / pyMLST
  whole genome MLST analysis
  ☆48Updated 3 months ago
• gbouras13 / plassembler
  Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates
  ☆76Updated last week
• wandreopoulos / deeplasmid
  ☆20Updated last year
• bonsai-team / Porechop_ABI
  Adapter trimmer for Oxford Nanopore reads using ab initio method
  ☆52Updated 10 months ago
• donovan-h-parks / CompareM
  A toolbox for comparative genomics.
  ☆104Updated 4 years ago
• cultivarium / MicrobeMod
  A toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing
  ☆49Updated last month
• katholt / RedDog
  ☆37Updated 3 years ago
• denglab / SeqSero2
  SeqSero2
  ☆38Updated last week
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆45Updated 5 years ago