Figure 1.

Overview of the splitcode workflow. The splitcode program takes in a set of FASTQ files and a user-specified config file, which serves as a recipe describing how the reads should be parsed. The user executes splitcode on the command-line, specifying command-line options on how the output should be formatted. The output consists of one or more of the following: the original FASTQ files (possibly edited), the extracted sequences (e.g. UMI sequences which are unknown and need to be extracted by using location information or anchor points), and the final barcodes which are unique for each combination of identified tags. The output may take the form of FASTQ files, gzip-compressed FASTQ files, BAM files, or interleaved sequences directed to standard output, depending on what the user specifies.