Alternatives and similar repositories for Shotgun-Metagenomics-Analysis:

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

• karkman / MetagenomeCourse2019
  Course material for the metagenomics course
  ☆44Updated 3 years ago
• bhattlab / kraken2_classification
  Snakemake workflow for metagenomic classification with Kraken2
  ☆65Updated last year
• HCBravoLab / metagenomeSeq
  Statistical analysis for sparse high-throughput sequencing
  ☆69Updated 4 months 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…
  ☆54Updated 3 years ago
• ParkinsonLab / Metatranscriptome-Workshop
  Metatranscriptomics Tutorial
  ☆62Updated last year
• transcript / samsa2
  SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…
  ☆57Updated last year
• grimmlab / MicrobiomeBestPracticeReview
  Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
  ☆115Updated 11 months ago
• DeniRibicic / q2ONT
  Bash pipeline for analysis of ONT full-length 16S sequences in QIIME2
  ☆29Updated 5 years ago
• bjtully / BioData
  All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")
  ☆73Updated 2 years ago
• Finn-Lab / MAG_Snakemake_wf
  Recovery of prokaryotic genomes from shotgun metagenomic sequencing data
  ☆59Updated 4 years ago
• PacificBiosciences / HiFi-16S-workflow
  Nextflow pipeline to analyze PacBio HiFi full-length 16S data
  ☆75Updated 2 months ago
• christophertbrown / iRep
  scripts for estimating bacteria replication rates based on population genome copy number variation
  ☆72Updated 5 years ago
• biofuture / Ublastx_stageone
  This is the source code for multisamples ARGs profiling using SARG2.0 database
  ☆46Updated 4 years ago
• SegataLab / panphlan
  PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
  ☆45Updated last year
• Russel88 / DAtest
  Compare different differential abundance and expression methods
  ☆51Updated 3 years ago
• mdsufz / MuDoGeR
  MuDoGeR makes the recovery of genomes from prokaryotes, viruses, and eukaryotes from metagenomes easy.
  ☆88Updated 8 months ago
• SvetlanaUP / Microbiome-etc-Podcasts
  This repo collects the list of podcasts related to microbiome science: science, microbiology and bioinformatics.
  ☆29Updated 5 months ago
• hildebra / lotus2
  Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.
  ☆53Updated 3 months ago
• Finn-Lab / MGS-gut
  Analysing Metagenomic Species (MGS)
  ☆41Updated 4 years ago
• waldronlab / curatedMetagenomicDataAnalyses
  Analyses in R and Python Using curatedMetagenomicData
  ☆31Updated last month
• linxingchen / cobra
  A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during…
  ☆70Updated 8 months ago
• bhattlab / MGEfinder
  A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
  ☆117Updated last year
• WatsonLab / MAGpy
  Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
  ☆62Updated 2 years ago
• victoriapascal / gutsmash
  gutSMASH
  ☆53Updated 4 months ago
• benjjneb / LRASManuscript
  Reproducible Analyses accompanying DADA2 + PacBio Manuscript
  ☆33Updated 4 years ago
• Gibbons-Lab / isb_course_2023
  Materials and presentation for the 2023 ISB Microbiome course.
  ☆24Updated 7 months ago
• xiaoli-dong / metaerg
  ☆41Updated 4 years ago
• EBI-Metagenomics / mettannotator
  ☆70Updated this week
• ignasrum / hocort
  HoCoRT - Remove specific organisms from sequencing reads
  ☆17Updated 4 months ago
• rrwick / Metagenomics-Index-Correction
  ☆82Updated last year