v2.1

Major updates

• Add a final step to perform the read-to-whitelist assignment: A putative barcode (16nt) will first be extended to include flanking bases from both sides. Then we scan through the whitelist and find the one with the lowest subsequence edit distance (ED: defined as the minimum edits required to make a shorter sequence a subsequence of the longer one).
• Identifies the putative UMI sequences for each read The end position of the barcode, which is also the start position of the UMI sequence, will be corrected by taking into account the insertion and deletion errors in the putative barcode. The 10 (for 10x v2 kit) or 12nt (for 10x v3 kit) sequence immediately downstream will be used as UMI.
• Trim the bases before and included in UMI from the demultiplexed reads: The output format will be in fastq or fastq.gz. The header with be @<16 nt BC>_<12 nt UMI>#read_id_<strand>
• Significant runtime improvement (~5-10 times faster)

Minor updates

• --emptydrop option in v1.x is on by default and is no longer user-specified.
• Add more information to the putative barcode table:
  • putative UMI
  • UMI end position (used for later trimming the adaptor-UMI sequence from each read)
  • Flanking bases before barcode and after UMI (for correction of insertion and deletion within the putative barcode and UMIs)