Alternatives and similar repositories for referenceseeker

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

• bacpop / PopPUNK
  PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
  ☆100Updated 2 weeks ago
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆77Updated 3 years ago
• jhawkey / IS_mapper
  IS mapping software
  ☆56Updated 3 years ago
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆70Updated 4 years ago
• bvalot / pyMLST
  whole genome MLST analysis
  ☆46Updated 2 months ago
• gtonkinhill / panstripe
  post processing of bacterial pangenome gene presence/absence matrices
  ☆60Updated 6 months ago
• gbouras13 / dnaapler
  Reorients assembled microbial sequences
  ☆125Updated last week
• gem-pasteur / PanACoTA
  PANgenome with Annotations, COre identification, Tree and corresponding Alignments
  ☆74Updated last year
• MDU-PHL / abritamr
  A pipeline for running AMRfinderPlus and collating results into functional classes
  ☆80Updated last year
• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆76Updated 2 years ago
• simonrharris / SKA
  Split Kmer Analysis
  ☆65Updated 3 years ago
• bede / hostile
  Precise host read removal
  ☆103Updated 2 months ago
• fmalmeida / bacannot
  Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.
  ☆104Updated 5 months ago
• rrwick / Metagenomics-Index-Correction
  ☆84Updated last year
• linsalrob / PhiSpy
  Prediction of prophages from bacterial genomes
  ☆79Updated 2 months ago
• metagenlab / mummer2circos
  Circular bacterial genome plots based on BLAST or NUCMER/PROMER alignments
  ☆107Updated last year
• 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
  ☆50Updated last month
• rrwick / Verticall
  Recombination-free trees
  ☆59Updated 5 months ago
• vrmarcelino / CCMetagen
  Microbiome classification pipeline
  ☆66Updated 3 months ago
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆54Updated 2 years ago
• shenwei356 / gtdb-taxdump
  GTDB taxonomy taxdump files with trackable TaxIds
  ☆56Updated 4 months ago
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆46Updated 4 years ago
• gbouras13 / plassembler
  Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates
  ☆73Updated 2 months ago
• bacpop / ska.rust
  Split k-mer analysis – version 2
  ☆88Updated last month
• xavierdidelot / BactDating
  Bayesian inference of ancestral dates on bacterial phylogenetic trees
  ☆91Updated 3 weeks ago
• avierstr / amplicon_sorter
  Sorts amplicons from Nanopore sequencing data based on similarity
  ☆38Updated 2 months ago
• donovan-h-parks / CompareM
  A toolbox for comparative genomics.
  ☆104Updated 4 years ago
• BU-ISCIII / plasmidID
  PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identifi…
  ☆42Updated 4 years ago
• WatsonLab / MAGpy
  Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
  ☆62Updated 2 years ago