Alternatives and similar repositories for q2-fondue:

Users that are interested in q2-fondue are comparing it to the libraries listed below

• CAMI-challenge / OPAL
  OPAL: Open-community Profiling Assessment tooL
  ☆28Updated 2 months ago
• gregpoore / tcga_rebuttal
  Re-analysis of data provided by Gihawi et al. 2023 bioRxiv
  ☆26Updated last year
• biocore / BIRDMAn
  Bayesian Inferential Regression for Differential Microbiome Analysis
  ☆22Updated last year
• Arcadia-Science / seqqc
  A Nextflow pipeline to identify quality control issues with new sequencing data.
  ☆28Updated 2 years ago
• fulcrumgenomics / fqtk
  Fast FASTQ sample demultiplexing in Rust.
  ☆60Updated 2 weeks ago
• KevinKuchinski / ProbeTools
  Hybridization probe design for targeted genomic sequencing of diverse and hypervariable viral taxa
  ☆23Updated last year
• biocore / DEICODE
  Robust Aitchison PCA from sparse count data
  ☆33Updated 2 years ago
• FredHutch / workflow-template-nextflow
  Template for building a small workflow in Nextflow
  ☆16Updated 2 years ago
• zavolanlab / zarp
  The Zavolab Automated RNA-seq Pipeline
  ☆35Updated 2 weeks ago
• frubino / mgkit
  MGKit: Metagenomics Framework
  ☆17Updated 2 years ago
• rhpvorderman / sequali
  Fast sequencing data quality metrics
  ☆26Updated this week
• FEI38750 / MTD
  MTD: a unique pipeline for host and meta-transcriptome joint and integrative analyses of RNA-seq data
  ☆16Updated 10 months ago
• pachterlab / fastQpick
  ☆25Updated last month
• linsalrob / SRA_Metadata
  Get, parse, and extract information from the SRA metadata files
  ☆38Updated 2 years ago
• mribeirodantas / NextflowSnippets
  This repository hosts a large collection of Nextflow snippets
  ☆57Updated 2 months ago
• SamStudio8 / majora2
  Malleable All-seeing Journal Of Research Artifacts
  ☆36Updated last year
• sandberg-lab / Spreading-Correction
  Supplementary information to "Computational correction of index switching in multiplexed sequencing libraries" (Larsson et. al 2018).
  ☆15Updated 4 years ago
• jsh58 / NGmerge
  Merging paired-end reads and removing adapters
  ☆44Updated 2 weeks ago
• YuLab-SMU / MicrobiomeProfiler
  A shiny package for microbiome functional enrichment analysis
  ☆38Updated 5 months ago
• Kingsford-Group / squid
  SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data
  ☆42Updated 2 years ago
• niemasd / ViralMSA
  Reference-guided multiple sequence alignment of viral genomes
  ☆65Updated 2 months ago
• leylabmpi / endoR
  Code and manual of the endoR R-package (Ruaud et al, in preparation).
  ☆12Updated last year
• ToniWestbrook / paladin
  Protein Alignment and Detection Interface
  ☆61Updated last year
• OceanGenomics / mudskipper
  A tool for projecting genomic alignments to transcriptomic coordinates
  ☆35Updated 10 months ago
• MHH-RCUG / Wochenende
  Deprecated see https://github.com/MHH-RCUG/nf_wochenende : A whole Genome/Metagenome Sequencing Alignment Pipeline in Python3
  ☆36Updated 2 years ago
• Gibbons-Lab / mbtools
  R package for microbiome analysis. Provides helper functions for common workflows ranging from preprocessing to visualization.
  ☆23Updated last year
• grenaud / deML
  Maximum likelihood demultiplexing
  ☆46Updated last month
• chizksh / digenome-toolkit2
  Digenome-toolkit ver2.
  ☆16Updated 3 years ago
• TrinityCTAT / CTAT-VirusIntegrationFinder
  ☆15Updated last year
• eclarke / komplexity
  A method of assessing sequence complexity based on kmer frequencies
  ☆31Updated 6 years ago