Alternatives and similar repositories for Shotgun-Metagenomics-Analysis

Users that are interested in Shotgun-Metagenomics-Analysis are comparing it to the libraries listed below

• bhattlab / kraken2_classification
  Snakemake workflow for metagenomic classification with Kraken2
  ☆66Updated 2 years ago
• grimmlab / MicrobiomeBestPracticeReview
  Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
  ☆123Updated last year
• karkman / MetagenomeCourse2019
  Course material for the metagenomics course
  ☆47Updated 3 years ago
• transcript / samsa2
  SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…
  ☆61Updated last year
• Zymo-Research / figaro
  An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters
  ☆95Updated last year
• AstrobioMike / bit
  Bioinformatics Tools
  ☆90Updated this week
• ParkinsonLab / Metatranscriptome-Workshop
  Metatranscriptomics Tutorial
  ☆66Updated 2 years ago
• PacificBiosciences / HiFi-16S-workflow
  Nextflow pipeline to analyze PacBio HiFi full-length 16S data
  ☆90Updated 6 months ago
• nearinj / Comparison_of_DA_microbiome_methods
  ☆58Updated last year
• smdabdoub / kraken-biom
  Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…
  ☆57Updated 3 years ago
• biobakery / biobakery_workflows
  bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validate…
  ☆130Updated 3 months ago
• victoriapascal / gutsmash
  gutSMASH
  ☆57Updated 3 months ago
• nmquijada / tormes
  Making whole bacterial genome sequencing data analysis easy
  ☆114Updated 8 months ago
• biobakery / maaslin3
  MaAsLin3: Microbiome Multivariate Association with Linear Models
  ☆56Updated 2 months ago
• hzi-bifo / RiboDetector
  Accurate and rapid RiboRNA sequences Detector based on deep learning
  ☆116Updated last month
• waldronlab / curatedMetagenomicDataAnalyses
  Analyses in R and Python Using curatedMetagenomicData
  ☆33Updated 2 months ago
• bjtully / BioData
  All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")
  ☆80Updated 2 years ago
• segalab / SGVFinder
  ☆32Updated 2 years ago
• Finn-Lab / MAG_Snakemake_wf
  Recovery of prokaryotic genomes from shotgun metagenomic sequencing data
  ☆62Updated 4 years ago
• HCBravoLab / metagenomeSeq
  Statistical analysis for sparse high-throughput sequencing
  ☆71Updated last year
• SegataLab / lefse
  ☆87Updated last year
• ignasrum / hocort
  HoCoRT - Remove specific organisms from sequencing reads
  ☆17Updated last year
• benjjneb / LRASManuscript
  Reproducible Analyses accompanying DADA2 + PacBio Manuscript
  ☆34Updated 5 years ago
• AnantharamanLab / ViWrap
  A wrapper to identify, bin, classify, and predict host-viral relationship for viruses
  ☆85Updated last year
• DeniRibicic / q2ONT
  Bash pipeline for analysis of ONT full-length 16S sequences in QIIME2
  ☆29Updated 5 years ago
• bhattlab / MGEfinder
  A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
  ☆124Updated 2 years ago
• donovan-h-parks / STAMP
  Statistical Analysis of Metagenomic Profiles
  ☆94Updated 5 years ago
• motu-tool / mOTUs
  motus - a tool for marker gene-based OTU (mOTU) profiling
  ☆166Updated last month
• mgoeker / table2itol
  Generating iToL annotations from Spreadsheet or CSV files
  ☆107Updated 5 years ago
• scwatts / fastspar
  Rapid and scalable correlation estimation for compositional data
  ☆96Updated last year