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
  ☆70Updated 11 months ago
• bhattlab / bhattlab_workflows
  Computational workflows for metagenomics tasks, by the Bhatt lab
  ☆47Updated 2 years ago
• snayfach / MicrobeCensus
  MicrobeCensus estimates the average genome size of microbial communities from metagenomic data
  ☆45Updated 5 years ago
• lozuponelab / SCNIC
  Sparse Cooccurence Network Investigation for Compositional data
  ☆25Updated last year
• edamame-course / Metagenome
  ☆23Updated 7 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
  ☆66Updated last year
• WatsonLab / MAGpy
  Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
  ☆62Updated 2 years ago
• ToniWestbrook / paladin
  Protein Alignment and Detection Interface
  ☆60Updated last year
• Russel88 / DAtest
  Compare different differential abundance and expression methods
  ☆52Updated 3 years ago
• hildebra / lotus2
  Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.
  ☆53Updated 5 months ago
• MadsAlbertsen / mmgenome
  Please use mmgenome2 instead. Tools for extracting individual genomes from metagenomes
  ☆27Updated 8 years ago
• GATB / simka
  Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.
  ☆50Updated 3 years ago
• christophertbrown / iRep
  scripts for estimating bacteria replication rates based on population genome copy number variation
  ☆72Updated 5 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
• gjospin / PhyloSift
  Phylogenetic and taxonomic analysis for genomes and metagenomes
  ☆82Updated 9 years ago
• SegataLab / metamlst
  MetaMLST is a computational tool for in-silico Multi-Locus Sequence Typing from metagenomic data.
  ☆16Updated 2 years ago
• hzi-bifo / traitar
  From genomes to phenotypes: Traitar, the microbial trait analyzer
  ☆61Updated 6 years ago
• arumugamlab / msamtools
  Metagenomics-related extended functionalities to samtools
  ☆22Updated 2 years ago
• chrisquince / DESMAN
  De novo Extraction of Strains from MetAgeNomes
  ☆71Updated 5 years ago
• Lagkouvardos / Rhea
  A set of R scripts for the analysis of microbial profiles
  ☆41Updated last year
• benjjneb / LRASManuscript
  Reproducible Analyses accompanying DADA2 + PacBio Manuscript
  ☆33Updated 5 years ago
• leylabmpi / Struo2
  Scalable creating/updating of metagenome profiling databases
  ☆62Updated 4 months ago
• xiaoli-dong / metaerg
  ☆40Updated 4 years ago
• weisberglab / beav
  BEAV: Bacterial Element Annotation reVamped
  ☆72Updated 2 months ago
• knights-lab / BURST
  An ultrafast optimal aligner for mapping large NGS data to large genome databases.
  ☆57Updated last year
• lmrodriguezr / enveomics
  Scripts and libraries for Environmental Genomics
  ☆38Updated 9 months 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 3 years ago
• ctmrbio / stag-mwc
  StaG Metagenomic Workflow Collaboration
  ☆28Updated last year
• nextgenusfs / amptk
  AMPtk: Amplicon ToolKit for NGS data (formally UFITS)
  ☆39Updated 2 years ago
• hsgweon / pipits
  Automated pipeline for analyses of fungal ITS from the Illumina
  ☆31Updated 6 months ago