LR-splitpipe v2.0

New version of LR-splitpipe:

demultiplex.py

• Improves performance on larger sets of reads by reading and processing reads in chunks
• Option to just run the linker scoring so that linker mismatch can be chosen at later steps (score_linkers mode)
• Allows for processing of multiple fastq files to be aggregated at the barcode correction step (subsequent usage of find_bcs and process_bcs step)
• Added options to tune number of allowable mismatches in each linker
• Improved QC
• Removed option to filter on corresponding Illumina data
• Removed option to filter based on read count per barcpde
• Added UMI deduplication with keep the longest read heuristic

add_bam_tag.py

• Added option to append a suffix to each barcode. Useful if combining multiple SAM files from different experimentss down the line that might have overlapping barcodes

LR-splitpipe v1.0

Code to demultiplex long-read Split-seq data