Alternatives and similar repositories for pathogensurveillance

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

• rrwick / Verticall
  Recombination-free trees
  ☆59Updated 5 months ago
• mw55309 / ideel
  Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
  ☆54Updated 2 years ago
• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆43Updated 4 years ago
• wtmatlock / flanker
  Gene-flank analysis tool
  ☆29Updated 8 months ago
• flass / pantagruel
  a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
  ☆49Updated 2 years ago
• simonrharris / SKA
  Split Kmer Analysis
  ☆65Updated 3 years ago
• zheminzhou / PEPPAN
  Phylogeny Enhanded Prediction of PAN-genome
  ☆42Updated 5 years ago
• WatsonLab / MAGpy
  Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
  ☆62Updated 2 years ago
• gtonkinhill / fastbaps
  A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data
  ☆65Updated 2 years ago
• katholt / RedDog
  ☆36Updated 3 years ago
• bvalot / pyMLST
  whole genome MLST analysis
  ☆46Updated 2 months ago
• MadsAlbertsen / mmgenome
  Please use mmgenome2 instead. Tools for extracting individual genomes from metagenomes
  ☆27Updated 8 years ago
• taxprofiler / taxpasta
  TAXnomic Profile Aggregation and STAndardisation
  ☆41Updated last week
• bioinfo-ut / PlasmidSeeker
  A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
  ☆35Updated 4 years ago
• leylabmpi / Struo
  Ley Lab MetaGenome Profiler DataBase generator
  ☆50Updated 2 years ago
• weisberglab / beav
  BEAV: Bacterial Element Annotation reVamped
  ☆67Updated last week
• rrwick / Rebaler
  reference-based long read assemblies of bacterial genomes
  ☆50Updated 4 years ago
• microbial-pangenomes-lab / microGWAS
  Bacterial GWAS analysis
  ☆43Updated last month
• irycisBioinfo / PATO
  PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.
  ☆61Updated last year
• drpowell / FriPan
  Interactive, web tool for exploring pan-genome of bacterial strains
  ☆46Updated 2 years ago
• moshi4 / MGCplotter
  Microbial Genome Circular plotting tool for comparative genomics using Circos
  ☆38Updated 2 years ago
• rrwick / Core-SNP-filter
  a tool to filter sites in a FASTA-format whole-genome pseudo-alignment
  ☆60Updated 2 months ago
• sanger-pathogens / assembly_improvement
  Improve the quality of a denovo assembly by scaffolding and gap filling
  ☆56Updated 4 years ago
• nf-core / bactmap
  A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
  ☆59Updated last month
• adlape95 / Spaghetti
  Spaghetti: in situ analysis of 16S rRNA amplicons obtained by nanopore sequencing
  ☆18Updated last year
• shandley / hecatomb
  hecatomb is a virome analysis pipeline for analysis of Illumina sequence data
  ☆59Updated 3 months ago
• hoelzer-lab / ribap
  A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs
  ☆30Updated 10 months ago
• MigleSur / GenAPI
  Gene Absence Presence Identification tool.
  ☆27Updated 5 months ago
• kussell-lab / mcorr
  Inferring bacterial recombination rates from large-scale sequencing datasets.
  ☆43Updated 2 years ago
• insapathogenomics / ReporTree
  A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
  ☆37Updated 2 months ago