Alternatives and similar repositories for kraken-biom

Users that are interested in kraken-biom are comparing it to the libraries listed below

• rrwick / Metagenomics-Index-Correction
  ☆83Updated 2 years ago
• bhattlab / kraken2_classification
  Snakemake workflow for metagenomic classification with Kraken2
  ☆65Updated 2 years ago
• transcript / samsa2
  SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…
  ☆58Updated last year
• PacificBiosciences / HiFi-16S-workflow
  Nextflow pipeline to analyze PacBio HiFi full-length 16S data
  ☆83Updated 2 months ago
• DeniRibicic / q2ONT
  Bash pipeline for analysis of ONT full-length 16S sequences in QIIME2
  ☆29Updated 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 2 years ago
• Zymo-Research / figaro
  An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters
  ☆90Updated last year
• bhattlab / lathe
  A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
  ☆69Updated 4 years ago
• snayfach / MicrobeCensus
  MicrobeCensus estimates the average genome size of microbial communities from metagenomic data
  ☆45Updated 5 years ago
• tobiasgf / lulu
  r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)
  ☆71Updated last year
• shenwei356 / gtdb-taxdump
  GTDB taxonomy taxdump files with trackable TaxIds
  ☆55Updated 5 months 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
• karkman / MetagenomeCourse2019
  Course material for the metagenomics course
  ☆44Updated 3 years ago
• GiantSpaceRobot / FindFungi
  A pipeline for the identification of fungi in public metagenomics datasets
  ☆17Updated 4 years ago
• scwatts / fastspar
  Rapid and scalable correlation estimation for compositional data
  ☆93Updated last year
• songweizhi / MetaCHIP
  Horizontal gene transfer (HGT) identification pipeline
  ☆63Updated 2 years ago
• fanglab / nanodisco
  nanodisco: a toolbox for discovering and exploiting multiple types of DNA methylation from individual bacteria and microbiomes using nano…
  ☆70Updated 3 years ago
• bjtully / BioData
  All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")
  ☆77Updated 2 years ago
• mjsull / Easyfig
  Development version of Easyfig
  ☆100Updated last year
• AstrobioMike / bit
  Bioinformatics Tools
  ☆90Updated last week
• jhawkey / IS_mapper
  IS mapping software
  ☆56Updated 3 years ago
• WatsonLab / MAGpy
  Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
  ☆62Updated 2 years ago
• arumugamlab / msamtools
  Metagenomics-related extended functionalities to samtools
  ☆21Updated 2 years ago
• christophertbrown / iRep
  scripts for estimating bacteria replication rates based on population genome copy number variation
  ☆72Updated 5 years ago
• biobakery / maaslin3
  MaAsLin3: Microbiome Multivariate Association with Linear Models
  ☆47Updated this week
• vrmarcelino / CCMetagen
  Microbiome classification pipeline
  ☆65Updated 4 months ago
• xavierdidelot / BactDating
  Bayesian inference of ancestral dates on bacterial phylogenetic trees
  ☆91Updated 2 months ago
• knights-lab / SHOGUN
  SHallow shOtGUN profiler
  ☆53Updated 3 years ago
• treangenlab / emu
  ☆63Updated 2 months ago
• irycisBioinfo / PATO
  PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.
  ☆62Updated last year