Alternatives and similar repositories for micca

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

• SchlossLab / schtools
  Schloss Lab Tools for Reproducible Microbiome Research 💩
  ☆31Updated last year
• edamame-course / Metagenome
  ☆23Updated 6 years ago
• kbseah / genome-bin-tools
  Interactive tools for metagenome visualization and binning in R
  ☆28Updated 6 years ago
• nextgenusfs / amptk
  AMPtk: Amplicon ToolKit for NGS data (formally UFITS)
  ☆38Updated last year
• microsud / microbiomeutilities
  The is mostly a wrapper tool using phyloseq and microbiome R packages.
  ☆34Updated 2 years ago
• KasperSkytte / mmgenome2
  Tools for extracting individual genomes from metagenomes
  ☆17Updated last year
• hsgweon / pipits
  Automated pipeline for analyses of fungal ITS from the Illumina
  ☆31Updated 2 weeks ago
• MadsAlbertsen / mmgenome
  Please use mmgenome2 instead. Tools for extracting individual genomes from metagenomes
  ☆27Updated 7 years ago
• sanger-pathogens / gff3toembl
  Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI
  ☆29Updated 6 years ago
• mikemc / speedyseq
  Speedy versions of phyloseq functions
  ☆48Updated last year
• linsalrob / partie
  PARTIE is a program to partition sequence read archive (SRA) metagenomics data into amplicon and shotgun data sets. The user-supplied ann…
  ☆26Updated 2 years ago
• MG-RAST / matR
  Metagenomics Analysis Tools
  ☆25Updated 7 years ago
• schuyler-smith / phylosmith
  functions for analyzing phyloseq data
  ☆27Updated 3 months ago
• vallenderlab / MicrobiomeR
  A comprehensive and customizable R package for microbiome analysis.
  ☆23Updated 2 years ago
• chrisquince / DESMAN
  De novo Extraction of Strains from MetAgeNomes
  ☆68Updated 4 years ago
• MVesuviusC / primerTree
  PrimerTree: Visually Assessing the Specificity and Informativeness of Primer Pairs
  ☆52Updated last year
• vmaffei / dada2_to_picrust
  Experimental pipeline to perform de novo PICRUSt on de-noised amplicon sequence variants (ASV)
  ☆19Updated 6 years ago
• borenstein-lab / fishtaco
  FishTaco (Functional Shifts Taxonomic Contributors) is a metagenomic computational framework that aims to identify the driver taxa of mic…
  ☆24Updated 3 years ago
• dcdanko / MD2
  MicrobeDirectory 2.0
  ☆22Updated 4 years ago
• rdpstaff / classifier
  RDP extensible sequence classifier for fungal lsu, bacterial and archaeal 16s
  ☆57Updated 2 years ago
• benjjneb / LRASManuscript
  Reproducible Analyses accompanying DADA2 + PacBio Manuscript
  ☆33Updated 4 years ago
• geraldinepascal / FROGS
  FROGS is a galaxy/CLI workflow designed to produce an OTUs count matrix from high depth sequencing amplicon data.
  ☆31Updated last week
• claczny / VizBin
  Repository of our application for human-augmented binning
  ☆28Updated 4 years ago
• Askarbek-orakov / ASAR
  Advanced metagenomic Sequence Analysis in R
  ☆15Updated 6 years ago
• rdpstaff / fungene_pipeline
  Scripts and resources for analyzing sequence data for select eco-functional genes
  ☆20Updated 7 years ago
• OSS-Lab / MetQy
  Repository for R package MetQy (read related publication here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6247936/)
  ☆18Updated 3 years ago
• bhattlab / bhattlab_workflows
  Computational workflows for metagenomics tasks, by the Bhatt lab
  ☆47Updated 2 years ago
• twbattaglia / btools
  A set of R functions that help faciliate a lot of tedious processing
  ☆18Updated 6 years ago
• KasperSkytte / ampvis2
  Tools for visualising microbial community amplicon data
  ☆67Updated last month
• Lagkouvardos / Rhea
  A set of R scripts for the analysis of microbial profiles
  ☆41Updated 11 months ago