Alternatives and similar repositories for taxumap:

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

• kevsilva / StrainFLAIR
  Strain-level abundances estimation in metagenomic samples using variation graphs
  ☆25Updated 2 years ago
• ewissel / hAMRoaster
  hAMRoaster is an analysis pipeline that can compare the output of tools for detecting AMR genes and provide metrics of their performance
  ☆22Updated 11 months ago
• smangul1 / MiCoP
  MiCoP is a method for high-accuracy profiling of viral and fungal metagenomic communities.
  ☆15Updated 2 years ago
• lozuponelab / AMON
  Annotation of Metabolite Origin via Networks: A tool for predicting putative metabolite origins for microbes or between microbes and host…
  ☆21Updated 10 months ago
• maxibor / sam2lca
  Lowest Common Ancestor from a SAM/BAM/CRAM alignment file
  ☆9Updated 6 months ago
• EGTortuero / viga
  De novo VIral Genome Annotator
  ☆21Updated 5 months ago
• Gibbons-Lab / mbtools
  R package for microbiome analysis. Provides helper functions for common workflows ranging from preprocessing to visualization.
  ☆23Updated last year
• mmpust / raspir
  Raspir, the rare species identifier
  ☆11Updated last year
• katcoyte / MK-SpikeSeq
  Protocols, data and code associated with the MK-SpikeSeq method for quantifying the absolute abundances of microbiota samples
  ☆13Updated 3 years ago
• sharpton / shotmap
  A Shotgun Metagenome Annotation Pipeline
  ☆23Updated 7 years ago
• FredHutch / nf-anvio-pangenome
  Analyze a set of genomes with the anvi'o pangenome pipeline
  ☆17Updated last year
• xmuyulab / Snipe
  Highly sensitive pathogen detection
  ☆12Updated 4 years ago
• maxemil / PhyloMagnet
  screening metagenomes for arbitrary lineages, using gene-centric assembly methods and phylogenetics
  ☆11Updated 4 years ago
• biocore / greengenes2
  Processing support for Greengenes2
  ☆12Updated last year
• borenstein-lab / fishtaco
  FishTaco (Functional Shifts Taxonomic Contributors) is a metagenomic computational framework that aims to identify the driver taxa of mic…
  ☆24Updated 3 years ago
• nick-youngblut / traitar3
  From genomes to phenotypes: Traitar3, the microbial trait analyzer (for Python3)
  ☆22Updated 7 months ago
• pmenzel / taxonomy-tools
  C++ tools for NCBI taxonomy tasks
  ☆11Updated 3 years ago
• althonos / pyfastani
  Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.
  ☆22Updated last week
• rpetit3 / pasty
  A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates
  ☆12Updated 6 months ago
• KThorellGroup / BACTpipe
  BACTpipe: An assembly and annotation pipeline for bacterial genomics
  ☆20Updated 3 months ago
• DaehwanKimLab / seqwho
  SeqWho - A reliable and rapid FASTQ(A) file classifier
  ☆11Updated 3 years ago
• jgolob / maliampi
  Maximum Likelihood Amplicon Pipeline
  ☆22Updated 9 months ago
• AllTheBacteria / Phylign
  Map query sequences to the assemblies of all pre-June 2023 bacteria (https://ftp.ebi.ac.uk/pub/databases/AllTheBacteria/Releases/0.2/) on…
  ☆12Updated 9 months ago
• pixushi / tempted
  ☆14Updated 3 months ago
• GlobalPathogenAnalysisService / read-it-and-keep
  Read contamination removal
  ☆24Updated last year
• KoslickiLab / fmh-funprofiler
  A functional profiler for metagenomes using FracMinHash
  ☆16Updated 2 weeks ago
• dr-joe-wirth / primerForge
  software to identify primers that can distinguish genomes
  ☆21Updated last month
• quadram-institute-bioscience / dadaist2
  Dadaist2 🟨 Highway to R
  ☆13Updated last week
• davised / get_assemblies
  Download assembly files from NCBI
  ☆12Updated last year