Alternatives and similar repositories for SHOGUN

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

• HCBravoLab / metagenomeSeq
  Statistical analysis for sparse high-throughput sequencing
  ☆69Updated 6 months ago
• lozuponelab / SCNIC
  Sparse Cooccurence Network Investigation for Compositional data
  ☆24Updated 7 months ago
• hildebra / lotus2
  Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.
  ☆54Updated last week
• WatsonLab / MAGpy
  Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
  ☆62Updated 2 years ago
• benjjneb / LRASManuscript
  Reproducible Analyses accompanying DADA2 + PacBio Manuscript
  ☆32Updated 4 years ago
• edamame-course / Metagenome
  ☆23Updated 6 years ago
• GenomicsAotearoa / metagenomics_summer_school
  Course materials for the Genomics Aotearoa Metagenomics Summer School, to be hosted at the University of Auckland in Septermber
  ☆60Updated 9 months ago
• hsgweon / pipits
  Automated pipeline for analyses of fungal ITS from the Illumina
  ☆31Updated last month
• christophertbrown / iRep
  scripts for estimating bacteria replication rates based on population genome copy number variation
  ☆72Updated 5 years ago
• Russel88 / DAtest
  Compare different differential abundance and expression methods
  ☆51Updated 3 years ago
• gjospin / PhyloSift
  Phylogenetic and taxonomic analysis for genomes and metagenomes
  ☆82Updated 9 years ago
• snayfach / MicrobeCensus
  MicrobeCensus estimates the average genome size of microbial communities from metagenomic data
  ☆46Updated 5 years ago
• Lagkouvardos / Rhea
  A set of R scripts for the analysis of microbial profiles
  ☆41Updated last year
• statdivlab / radEmu
  ☆55Updated last month
• leylabmpi / Struo
  Ley Lab MetaGenome Profiler DataBase generator
  ☆50Updated 2 years ago
• a-h-b / dadasnake
  Amplicon sequencing workflow heavily using DADA2 and implemented in snakemake
  ☆48Updated last year
• SegataLab / panphlan
  PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
  ☆45Updated last year
• bhattlab / bhattlab_workflows
  Computational workflows for metagenomics tasks, by the Bhatt lab
  ☆47Updated 2 years ago
• microsud / microbiomeutilities
  The is mostly a wrapper tool using phyloseq and microbiome R packages.
  ☆34Updated 2 years ago
• weisberglab / beav
  BEAV: Bacterial Element Annotation reVamped
  ☆66Updated 7 months ago
• ctmrbio / stag-mwc
  StaG Metagenomic Workflow Collaboration
  ☆29Updated 10 months ago
• EnvGen / metagenomics-workshop
  Metagenomics Workshop
  ☆28Updated 8 years ago
• nextgenusfs / amptk
  AMPtk: Amplicon ToolKit for NGS data (formally UFITS)
  ☆38Updated last year
• geronimp / graftM
  GraftM - Rapid community profiles from metagenomes
  ☆45Updated 11 months ago
• jlw-ecoevo / gRodon
  ☆17Updated 2 years ago
• smdabdoub / kraken-biom
  Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…
  ☆55Updated 3 years ago
• ggloor / q2-aldex2
  qiime2 plugin for aldex2 for differential abundance analysis
  ☆11Updated 5 years ago
• transcript / samsa2
  SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…
  ☆56Updated last year
• mikemc / speedyseq
  Speedy versions of phyloseq functions
  ☆47Updated last year
• schuyler-smith / phylosmith
  functions for analyzing phyloseq data
  ☆28Updated 4 months ago