Alternatives and similar repositories for plasmidID

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

• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆77Updated 3 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
• jhawkey / IS_mapper
  IS mapping software
  ☆57Updated 4 years ago
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆69Updated 4 years ago
• aldertzomer / RFPlasmid
  Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf
  ☆50Updated last year
• Serka-M / mmlong2
  Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes
  ☆55Updated last month
• nekokoe / Plasmer
  An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features.
  ☆49Updated 2 years ago
• tseemann / phastaf
  Identify phage regions in bacterial genomes for masking purposes
  ☆34Updated 6 years ago
• denglab / SeqSero2
  SeqSero2
  ☆39Updated 2 months ago
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆81Updated 3 years ago
• gtonkinhill / panstripe
  post processing of bacterial pangenome gene presence/absence matrices
  ☆63Updated 9 months ago
• avierstr / amplicon_sorter
  Sorts amplicons from Nanopore sequencing data based on similarity
  ☆40Updated 2 months ago
• phac-nml / sistr_cmd
  SISTR (Salmonella In Silico Typing Resource) command-line tool
  ☆32Updated 7 months ago
• adlape95 / Assembly-methods-nanopore
  Assembly methods for nanopore-based metagenomic sequencing: a comparative study
  ☆18Updated 5 years ago
• egonozer / in_silico_pcr
  Perl script for simulating PCR reactions. Extract sequences from a query based on primer sequences.
  ☆48Updated 8 months ago
• linsalrob / PhiSpy
  Prediction of prophages from bacterial genomes
  ☆82Updated 5 months ago
• leylabmpi / Struo
  Ley Lab MetaGenome Profiler DataBase generator
  ☆50Updated 3 years ago
• DeniRibicic / q2ONT
  Bash pipeline for analysis of ONT full-length 16S sequences in QIIME2
  ☆29Updated 5 years ago
• cultivarium / MicrobeMod
  A toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing
  ☆51Updated last week
• simonrharris / SKA
  Split Kmer Analysis
  ☆65Updated 3 years ago
• katholt / RedDog
  ☆37Updated 3 years ago
• bvalot / pyMLST
  whole genome MLST analysis
  ☆50Updated 5 months ago
• gem-pasteur / PanACoTA
  PANgenome with Annotations, COre identification, Tree and corresponding Alignments
  ☆76Updated 2 years ago
• Shamir-Lab / SCAPP
  SCAPP is a plasmid assembly tool. This tool is described in our paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s4016…
  ☆34Updated 2 years ago
• zheminzhou / EToKi
  all methods related to Enterobase
  ☆43Updated last year
• MDU-PHL / abritamr
  A pipeline for running AMRfinderPlus and collating results into functional classes
  ☆90Updated last week
• shenwei356 / gtdb-taxdump
  GTDB taxonomy taxdump files with trackable TaxIds
  ☆56Updated 7 months ago
• LomanLab / EBAME18
  Long read metagenomics practical at EBAME18
  ☆18Updated 7 years ago
• SegataLab / panphlan
  PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
  ☆46Updated 2 years ago
• SWittouck / SCARAP
  A toolkit for prokaryotic comparative genomics
  ☆51Updated last month