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)

  • prepare pacbio data
  • quality stat
  • split read
  • unify sequence
  • call mutation

• Single Cell Tree Construction (tree)

  • build tree by maximum likelihood method
  • visualize tree
  • benchmarking cell lineage tracing system (tree/benchmark)

• Population Dynamics (pop)

  • ?

• simulation (simu)

READ MORE

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

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

How to use?

git clone --recurse-submodules https://github.com/CellLineage/SLOTH.git

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TODO

• turn consensus part into a independent package
• write wiki page for the technical details
• write web page for the scientific question
• add js framework for renderng the tree

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.