Alternatives and similar repositories for StrainFinder

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

• christophertbrown / iRep
  scripts for estimating bacteria replication rates based on population genome copy number variation
  ☆72Updated 5 years ago
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆69Updated 4 years ago
• leylabmpi / Struo
  Ley Lab MetaGenome Profiler DataBase generator
  ☆49Updated 2 years ago
• snayfach / MAGpurify
  Improvement of metagenome-assembled genomes
  ☆53Updated 5 years ago
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆45Updated 5 years ago
• xiaoli-dong / metaerg
  ☆40Updated 4 years ago
• hzi-bifo / traitar
  From genomes to phenotypes: Traitar, the microbial trait analyzer
  ☆60Updated 6 years ago
• shenwei356 / gtdb-taxdump
  GTDB taxonomy taxdump files with trackable TaxIds
  ☆55Updated 4 months ago
• snayfach / MicrobeCensus
  MicrobeCensus estimates the average genome size of microbial communities from metagenomic data
  ☆45Updated 5 years ago
• simonrharris / SKA
  Split Kmer Analysis
  ☆65Updated 3 years ago
• SWittouck / SCARAP
  A toolkit for prokaryotic comparative genomics
  ☆50Updated 7 months ago
• WatsonLab / MAGpy
  Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
  ☆62Updated 2 years ago
• linsalrob / PhiSpy
  Prediction of prophages from bacterial genomes
  ☆79Updated 3 months ago
• lmrodriguezr / nonpareil
  Estimate metagenomic coverage and sequence diversity
  ☆54Updated last year
• vrmarcelino / CCMetagen
  Microbiome classification pipeline
  ☆65Updated 4 months ago
• leylabmpi / Struo2
  Scalable creating/updating of metagenome profiling databases
  ☆62Updated 2 months ago
• Finn-Lab / MGS-gut
  Analysing Metagenomic Species (MGS)
  ☆41Updated 4 years ago
• knights-lab / BURST
  An ultrafast optimal aligner for mapping large NGS data to large genome databases.
  ☆57Updated last year
• donovan-h-parks / RefineM
  A toolbox for improving metagenome-assembled genomes.
  ☆62Updated 4 years ago
• functional-dark-side / agnostos-wf
  ☆45Updated 2 years ago
• FOI-Bioinformatics / flextaxd
  FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomi…
  ☆67Updated 6 months ago
• chrisquince / DESMAN
  De novo Extraction of Strains from MetAgeNomes
  ☆70Updated 5 years ago
• rrwick / Metagenomics-Index-Correction
  ☆83Updated 2 years ago
• rrwick / Bacsort
  a collection of scripts for organising bacterial genomes by species
  ☆76Updated 3 years ago
• rrwick / Assembly-Dereplicator
  A tool for removing redundant genomes from a set of assemblies
  ☆76Updated last week
• SegataLab / panphlan
  PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
  ☆44Updated last year
• philarevalo / PopCOGenT
  Microbial Populations as Clusters Of Gene Transfer
  ☆43Updated last year
• ToniWestbrook / paladin
  Protein Alignment and Detection Interface
  ☆60Updated last year
• ziyewang / MetaBinner
  ☆57Updated last year
• nick-youngblut / gtdb_to_taxdump
  Convert GTDB taxonomy to NCBI taxdump format
  ☆73Updated 2 years ago