Alternatives and similar repositories for seer

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

• chrisquince / STRONG
  Strain Resolution ON Graphs
  ☆48Updated 2 years ago
• sgearle / bugwas
  Locus and lineage tests for bacterial GWAS
  ☆29Updated 7 years ago
• phac-nml / refseq_masher
  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database
  ☆42Updated 4 years ago
• will-rowe / groot
  A resistome profiler for Graphing Resistance Out Of meTagenomes
  ☆66Updated 5 years ago
• karel-brinda / Phylign
  Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)
  ☆37Updated last year
• CAMI-challenge / CAMITAX
  CAMITAX: Taxon labels for microbial genomes
  ☆30Updated last year
• hzi-bifo / Haploflow
  ☆31Updated last year
• Gardner-BinfLab / deltaBS
  Quantifying the significance of genetic variation using probabilistic profile-based methods.
  ☆19Updated 4 years ago
• CAMI-challenge / OPAL
  OPAL: Open-community Profiling Assessment tooL
  ☆30Updated 7 months ago
• drpowell / FriPan
  Interactive, web tool for exploring pan-genome of bacterial strains
  ☆46Updated 2 years ago
• tseemann / ekidna
  Assembly based core genome SNP alignments for bacteria
  ☆25Updated 5 years ago
• bioinfo-ut / PhenotypeSeeker
  Identify phenotype-specific k-mers and predict phenotype using sequenced bacterial strains
  ☆19Updated 4 months ago
• sanger-pathogens / mlst_check
  Multilocus sequence typing by blast using the schemes from PubMLST
  ☆30Updated 3 years ago
• kevsilva / StrainFLAIR
  Strain-level abundances estimation in metagenomic samples using variation graphs
  ☆25Updated 2 years ago
• nlapier2 / Metalign
  Metalign: efficient alignment-based metagenomic profiling via containment min hash
  ☆34Updated last year
• marbl / MetaCompass
  MetaCompass: Reference-guided Assembly of Metagenomes
  ☆39Updated 3 weeks ago
• atifrahman / HAWK
  Hitting associations with k-mers
  ☆45Updated 3 years ago
• uio-cels / NucDiff
  In-depth characterization and annotation of differences between two sets of DNA sequences
  ☆62Updated 5 years ago
• rki-mf1 / clean
  A nextflow pipeline for decontamination of short reads, long reads and contigs
  ☆53Updated 2 months ago
• jessiewu / bacterialGWAS
  A pipeline for performing genome-wide association tests for bacterial genomes.
  ☆27Updated 7 years ago
• pirovc / metameta
  ☆23Updated 5 years ago
• pirovc / multitax
  Python package to obtain, parse and explore biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)
  ☆46Updated 2 months ago
• kamimrcht / REINDEER
  REINDEER REad Index for abuNDancE quERy
  ☆57Updated 2 months ago
• broadinstitute / StrainGE
  strain-level analysis tools
  ☆39Updated 10 months ago
• shenwei356 / unikmer
  A versatile toolkit for k-mers with taxonomic information
  ☆80Updated last week
• rvicedomini / strainberry
  Automated strain separation of low-complexity metagenomes
  ☆51Updated 3 years ago
• LANL-Bioinformatics / PhaME
  Given a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to constr…
  ☆33Updated last year
• bacpop / mandrake
  Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding
  ☆38Updated 6 months ago
• zheminzhou / PEPPAN
  Phylogeny Enhanded Prediction of PAN-genome
  ☆42Updated 5 years ago
• EvolBioInf / fur
  Find Unique genomic Regions
  ☆30Updated last week