y9c / sloth

Single-cell Lineage on Targeted Hypermutation

SLOTH (Single-cell Lineage on Targeted Hypermutation)

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Mapping single-cell-resolution cell phylogeny reveals cell population dynamics during organ developments

PROCEDURE

• Single Molecule Sequecing Pipeline (smrt)

  • Adaptors Trimming
  • Circular Consensus Sequence Generation
  • Align to Reference Sequence
  • Annotate Sequence Features
  • Link Sample Barcode Sequence
  • Cluster Molecular Indentifier (UMI) Sequence
  • Group Reads by Sample Barcode and Molecular Indentifier
  • Generate Consensus Sequence for Lineage Barcode
  • Call Mutation
  • Post Quality Filter

• Single Cell Tree Construction (tree)

  • Build Tree by Maximum Likelihood Method
  • Fix Tree
  • Visualize Tree

• Benchmarking Cell Lineage Tracing System (benchmark)

  • alemany_whole-organism_2018
  • bowling_engineered_2020
  • chan_molecular_2019
  • chen_efficient_2020
  • kalhor_developmental_2018
  • lee-six_population_2018
  • mckenna_whole-organism_2016
  • pei_polylox_2017
  • quinn_single-cell_2021
  • raj_simultaneous_2018
  • spanjaard_simultaneous_2018

• Simulation (simu)

  • Generate Cell Tree (division / differentiation / mutation)
  • Subsample Barcoded Cells
  • Reconstruct Cell Lineage Tree

• Population Dynamics (pop)

  • ?

READ MORE

scientific question : https://celllineage.github.io/SLOTH/index.html

technical details: https://github.com/CellLineage/SLOTH/wiki

HOW TO USE?

git clone https://github.com/CellLineage/SLOTH.git

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CITATION

Liu, K., Deng, S., Ye, C. et al. Mapping single-cell-resolution cell phylogeny reveals cell population dynamics during organ development. Nat Methods 18, 1506–1514 (2021). https://doi.org/10.1038/s41592-021-01325-x

LICENSE

The content of this project itself is created by Ye Chang and licensed under the Creative Commons Attribution 4.0 International License (CC BY), and the underlying source code used to format and display that content is licensed under the MIT license.