splitcode

splitcode is a tool for flexible, efficient parsing, interpreting, and editing of technical sequences in sequencing reads.

Introduction:

• Getting started
  • Installation
  • Graphical User Interface (GUI)
  • Command-line structure
  • Overview
  • Basic usage
• Example
  • Read structure
  • Config File
  • Sample Reads
  • Command-Line Run
  • Output
  • Colab

Contents:

• User guide: Tags
• User guide: Extraction
• Extracting from read names
• Random sequence insertion
• Nesting config files
• Header and SAM tags
• Streaming and Interleaving
• Demultiplexing
• Remultiplexing
• Reference guide
• Frequently asked questions

Tutorials:

• Put technical sequences into separate files
• Demultiplex single-cells into individual files
• Deduplication by barcode
• Separating Smart-seq3 reads
• SPLiT-seq processing
• SPRITE barcodes
• inDrops guide

Additional Features:

• Lift
• BAM output
• Unmasking

Citation:

Sullivan DK, Pachter L. (2024). Flexible parsing, interpretation, and editing of technical sequences with splitcode. Bioinformatics. https://doi.org/10.1093/bioinformatics/btae331