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 7 months ago
• bhattlab / bhattlab_workflows
  Computational workflows for metagenomics tasks, by the Bhatt lab
  ☆47Updated 2 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
  ☆62Updated 11 months ago
• WatsonLab / MAGpy
  Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
  ☆62Updated 2 years ago
• snayfach / MicrobeCensus
  MicrobeCensus estimates the average genome size of microbial communities from metagenomic data
  ☆46Updated 5 years ago
• hildebra / lotus2
  Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.
  ☆54Updated last month
• transcript / samsa2
  SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…
  ☆55Updated last year
• Russel88 / DAtest
  Compare different differential abundance and expression methods
  ☆51Updated 3 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…
  ☆56Updated 3 years ago
• hsgweon / pipits
  Automated pipeline for analyses of fungal ITS from the Illumina
  ☆31Updated 3 months ago
• christophertbrown / iRep
  scripts for estimating bacteria replication rates based on population genome copy number variation
  ☆72Updated 5 years ago
• zoecastillo / microbiomeExplorer
  The Microbiome Explorer provides methods to analyze and visualize microbial community sequencing data either from the R command line or t…
  ☆72Updated 2 years ago
• aomlomics / tourmaline
  Amplicon sequence processing workflow using QIIME 2 and Snakemake
  ☆47Updated this week
• benjjneb / LRASManuscript
  Reproducible Analyses accompanying DADA2 + PacBio Manuscript
  ☆32Updated 4 years ago
• lozuponelab / SCNIC
  Sparse Cooccurence Network Investigation for Compositional data
  ☆24Updated 9 months ago
• edamame-course / Metagenome
  ☆23Updated 7 years ago
• jlw-ecoevo / gRodon
  ☆17Updated 2 years ago
• ToniWestbrook / paladin
  Protein Alignment and Detection Interface
  ☆61Updated last year
• snayfach / IGGdb
  Database of genomes integrated from the gut microbiome and other environments
  ☆45Updated 2 years ago
• GATB / simka
  Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.
  ☆48Updated 3 years ago
• caitiecollins / treeWAS
  treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes
  ☆103Updated 6 months ago
• geronimp / graftM
  GraftM - Rapid community profiles from metagenomes
  ☆46Updated last year
• a-h-b / dadasnake
  Amplicon sequencing workflow heavily using DADA2 and implemented in snakemake
  ☆49Updated last year
• knights-lab / BURST
  An ultrafast optimal aligner for mapping large NGS data to large genome databases.
  ☆58Updated last year
• statdivlab / radEmu
  ☆56Updated last week
• MadsAlbertsen / mmgenome
  Please use mmgenome2 instead. Tools for extracting individual genomes from metagenomes
  ☆27Updated 7 years ago
• tobiasgf / lulu
  r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)
  ☆67Updated 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
• hzi-bifo / traitar
  From genomes to phenotypes: Traitar, the microbial trait analyzer
  ☆59Updated 5 years ago
• gjospin / PhyloSift
  Phylogenetic and taxonomic analysis for genomes and metagenomes
  ☆82Updated 9 years ago