scarecrow

A library-agnostic toolkit for pre-processing combinatorial indexed single-cell RNA sequence data.

• Installation
• Introduction
• Troubleshooting
• Examples
  • Parse Evercode WTv2
  • Scale QuantumnScale RNA
  • Scarecrow paper code
• Toolkit
  • encode
  • harvest
  • json
  • reap
  • recast
  • seed
  • sift
  • stats
  • weed

To-do

• Jitter does not currently apply to UMI or insert sequence
  • if UMI on same read as barcodes, and downstream of any, then position may need adjusting dynamically before extracting sequence and qualities

Wishlist

• Some tools would benefit from multi-threading (i.e. recast, stats)
• Would be helpful if weed could be refactored to work on FASTQ input format rather than just SAM