Alternatives and similar repositories for referenceseeker

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

• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆81Updated 3 years ago
• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆78Updated 5 months ago
• jhawkey / IS_mapper
  IS mapping software
  ☆57Updated 4 years ago
• bacpop / PopPUNK
  PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
  ☆103Updated this week
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆68Updated 4 years ago
• rrwick / Metagenomics-Index-Correction
  ☆84Updated 2 years ago
• gem-pasteur / PanACoTA
  PANgenome with Annotations, COre identification, Tree and corresponding Alignments
  ☆80Updated 2 years ago
• gbouras13 / dnaapler
  Reorients assembled microbial sequences
  ☆132Updated 5 months ago
• oschwengers / asap
  A scalable bacterial genome assembly, annotation and analysis pipeline
  ☆74Updated 2 years ago
• MDU-PHL / abritamr
  A pipeline for running AMRfinderPlus and collating results into functional classes
  ☆91Updated 2 months ago
• gtonkinhill / panstripe
  post processing of bacterial pangenome gene presence/absence matrices
  ☆63Updated 3 weeks ago
• xavierdidelot / BactDating
  Bayesian inference of ancestral dates on bacterial phylogenetic trees
  ☆94Updated 2 months ago
• shenwei356 / gtdb-taxdump
  GTDB taxonomy taxdump files with trackable TaxIds
  ☆57Updated 9 months ago
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆46Updated 5 years ago
• bede / hostile
  Precise host read removal
  ☆115Updated 5 months ago
• bacpop / ska.rust
  Split k-mer analysis – version 2
  ☆104Updated 2 weeks ago
• xavierdidelot / ClonalFrameML
  ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
  ☆120Updated last year
• SionBayliss / PIRATE
  A toolbox for pangenome analysis and threshold evaluation.
  ☆99Updated 3 years ago
• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆36Updated 5 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
• avierstr / amplicon_sorter
  Sorts amplicons from Nanopore sequencing data based on similarity
  ☆41Updated 4 months ago
• Serka-M / mmlong2
  Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes
  ☆55Updated 3 months ago
• simonrharris / SKA
  Split Kmer Analysis
  ☆67Updated 3 years ago
• marbl / parsnp
  Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can b…
  ☆149Updated 4 months ago
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆54Updated 2 years ago
• bacpop / ggCaller
  Bifrost graph gene caller.
  ☆98Updated 3 weeks ago
• hzi-bifo / traitar
  From genomes to phenotypes: Traitar, the microbial trait analyzer
  ☆65Updated 6 years ago
• linsalrob / PhiSpy
  Prediction of prophages from bacterial genomes
  ☆81Updated last week
• voorloopnul / awesome-phages
  A curated list of phage related software and computational resources for phage scientists, bioinformaticians and enthusiasts.
  ☆49Updated 3 years ago
• bonsai-team / Porechop_ABI
  Adapter trimmer for Oxford Nanopore reads using ab initio method
  ☆55Updated last year