Trimmer: Automated Read Processing on the UG 100® Sequencing Platform

Ultima Sequencing platforms on-board informatics will run Trimmer to separate the reads from a wafer into one file per UG Barcode (UGBC). Trimer functions include: • Trimming: Remove all the bases from a read that are unused during secondary analysis, such as those from adapters, spacers, A-overhangs and poly-T regions. • Demultiplexing: Tag all the reads that contain the same sample barcode(s) into a specific read group. Then run Demux to create one file per sample, according to the sample-specific read groups set by Trimmer. • Filtering: Tag all the reads that do not have the expected library structure so they can be discarded or reprocessed. These reads could be the result of library prep issues (insert too short or too long), sequencing quality/errors, contamination or run setup issues. In the latter case, reads can be easily reprocessed with a different configuration for troubleshooting. • Labelling: Tag each read with the name or sequence of any pattern they contain, such as a UMI or a cell barcode, so that the information can be leveraged by the downstream data analysis pipeline. For example, group reads into UMI families when doing somatic variant calling, or group reads with the same cell barcode together when doing single cell RNA-seq. Custom labels are also possible for annotation. • Formatting: When a pattern is identified in a read that corresponds to an expected Insert segment in the library, that segment is usually kept as is. But it can also be reformatted by size trimming or reverse complementation. This is useful if the downstream analysis expects paired-end reads in FASTQ format. • Reporting: Produces statistics on the number of reads matching an expected library structure or filtered.