kallisto | bustools

Overview:

  • Introduction
  • Background
  • References
  • Dependents

Quick Start:

  • Installing kb-python
  • The kb-python workflow

Index generation:

  • Generate a reference index

Bulk RNA seq:

  • Pseudoalignment of bulk RNA seq data
  • Tutorials

Single-cell RNA seq:

  • Pseudoalignment of single-cell RNA seq data
  • Technologies and the -x string
  • Tutorials
    • Introduction to single-cell RNA-seq: Seurat (R)
    • Introduction to single-cell RNA-seq: Scanpy (python)
    • Introduction to single-nucleus RNA-seq: Scanpy (python)
    • Nascent and Mature RNA quantification
    • SPLIT-Seq preprocessing

Long read RNA seq:

  • Long read pseudoaligment
  • Tutorials

Translated alignment:

  • Pseudoalignment of RNA seq data against a protein reference
  • Tutorials

seqspec:

  • seqspec

Troubleshooting:

  • Interpreting quality and run information

Manuals:

  • kallisto
  • bustools
  • kb-python

Advanced installation:

  • Installing from source
  • Releases

Advanced bustools:

  • Barcodes on-list format

FAQ:

  • Frequently asked questions
kallisto | bustools
  • Tutorials
  • Edit on GitHub

Tutorials

  • Introduction to single-cell RNA-seq: Seurat (R)
  • Introduction to single-cell RNA-seq: Scanpy (python)
  • Introduction to single-nucleus RNA-seq: Scanpy (python)
  • Nascent and Mature RNA quantification
  • SPLIT-Seq preprocessing
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