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All Projects → Taiji-pipeline → Taiji

Taiji-pipeline / Taiji

Licence: BSD-3-Clause license
All-in-one analysis pipeline

Programming Languages

haskell
3896 projects

Labels

transcriptional-regulatory-networksingle-cell-rna-seqrna-seq-pipelinesingle-cell-atac-seqatac-seq-pipeline

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Taiji -- multi-omics bioinformatics pipeline

GitHub release (latest by date including pre-releases) Continuous integration GitHub All Releases

Taiji is an integrative analysis pipeline for analyzing bulk/single-cell ATAC-seq and RNA-seq data. Please go to this website for documentation and tutorials.

  • Joint analysis of ATAC-seq, RNA-seq and Hi-C datasets.
  • Integrate multiple single cell datasets, scale to more than 1 million cells!

The design philosophy of the Taiji pipeline is focused on:

  • Correctness: We only include reliable algorithms and make every effort to ensure the implementations are bug-free.
  • Performance: We code algorithms from scratch when necessary to ensure the pipeline can scale to large datasets (thousands of samples at least).
  • Convinence: Most analyses have multipe entry points, e.g., Fastq, Bam or Bed. The execution of the pipeline requires only a single command.

We achieve these at the expense of customization. This will be improved in the future.

Installation

Pre-built binaries are available for macOS and Linux system:

  • taiji-CentOS-x86_64: for Red Hat Enterprise Linux derivatives.

  • taiji-Ubuntu-x86_64: for Debian linux derivatives.

  • taiji-macOS-XX-XX: for macOS.

Example:

curl -L https://github.com/Taiji-pipeline/Taiji/releases/latest/download/taiji-CentOS-x86_64 -o taiji
chmod +x taiji
./taiji --help

If you have used Taiji in your research, please consider citing the following paper:

K. Zhang, M. Wang, Y. Zhao, W. Wang, Taiji: System-level identification of key transcription factors reveals transcriptional waves in mouse embryonic development. Sci. Adv. 5, eaav3262 (2019).

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