PISA

PISA is designed for single-cell experiments. It's a collection of programs to process FASTQ and BAM files, including annotation, barcode correction, feature counting, and more. The idea of PISA is trying to integrate cell barcodes and molecular barcodes (UMIs) into plain FASTQ, the FASTQ+ format, but without changing its original property. Users could use current-state-of-art software to perform quality control, alignment, or even assembly for the FASTQ+ without a further update.