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
  ☆70Updated 3 years ago
• chrisquince / DESMAN
  De novo Extraction of Strains from MetAgeNomes
  ☆71Updated 5 years ago
• leylabmpi / Struo
  Ley Lab MetaGenome Profiler DataBase generator
  ☆50Updated 2 years ago
• shenwei356 / gtdb-taxdump
  GTDB taxonomy taxdump files with trackable TaxIds
  ☆56Updated 3 months ago
• hzi-bifo / traitar
  From genomes to phenotypes: Traitar, the microbial trait analyzer
  ☆59Updated 5 years ago
• lmrodriguezr / nonpareil
  Estimate metagenomic coverage and sequence diversity
  ☆54Updated last year
• snayfach / MicrobeCensus
  MicrobeCensus estimates the average genome size of microbial communities from metagenomic data
  ☆46Updated 5 years ago
• linsalrob / PhiSpy
  Prediction of prophages from bacterial genomes
  ☆79Updated last month
• leylabmpi / Struo2
  Scalable creating/updating of metagenome profiling databases
  ☆61Updated last month
• jordanlab / stringMLST
  Fast k-mer based tool for multi locus sequence typing (MLST)
  ☆46Updated 4 years ago
• FOI-Bioinformatics / flextaxd
  FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomi…
  ☆66Updated 4 months ago
• snayfach / MAGpurify
  Improvement of metagenome-assembled genomes
  ☆54Updated 5 years ago
• SegataLab / panphlan
  PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
  ☆45Updated last year
• SWittouck / SCARAP
  A toolkit for prokaryotic comparative genomics
  ☆50Updated 6 months ago
• vrmarcelino / CCMetagen
  Microbiome classification pipeline
  ☆66Updated 2 months ago
• ziyewang / MetaBinner
  ☆56Updated last year
• functional-dark-side / agnostos-wf
  ☆46Updated 2 years ago
• nick-youngblut / gtdb_to_taxdump
  Convert GTDB taxonomy to NCBI taxdump format
  ☆74Updated last year
• WatsonLab / MAGpy
  Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
  ☆62Updated 2 years ago
• rrwick / Metagenomics-Index-Correction
  ☆83Updated last year
• knights-lab / BURST
  An ultrafast optimal aligner for mapping large NGS data to large genome databases.
  ☆58Updated last year
• donovan-h-parks / RefineM
  A toolbox for improving metagenome-assembled genomes.
  ☆63Updated 4 years ago
• GiantSpaceRobot / FindFungi
  A pipeline for the identification of fungi in public metagenomics datasets
  ☆16Updated 4 years ago
• lozuponelab / SCNIC
  Sparse Cooccurence Network Investigation for Compositional data
  ☆24Updated 9 months ago
• biobakery / shortbred
  ShortBRED is a pipeline to take a set of protein sequences, reduce them to a set of unique identifying strings ("markers"), and then sear…
  ☆31Updated 6 months ago
• songweizhi / Binning_refiner
  Improving genome bins through the combination of different binning programs
  ☆31Updated 2 years ago
• philarevalo / PopCOGenT
  Microbial Populations as Clusters Of Gene Transfer
  ☆44Updated last year
• liu-congcong / MetaDecoder
  An algorithm for clustering metagenomic sequences.
  ☆37Updated 4 months ago
• tseemann / phastaf
  Identify phage regions in bacterial genomes for masking purposes
  ☆34Updated 5 years ago