Glossary

A standard (usually compressed) file format for representing aligned reads. The file is a binary version of the Sequence Alignment Map file standard.

Base call files produced by Illumina sequencers.

An Illumina program that translates BCL files into FASTQ files and labels the resulting reads with the UMIs.

To derive a consensus read from all the reads in a Family.

To alter a UMI or positional grouping to make that grouping more accurate based on known valid UMIs and nearby Families.

Two families that originate from the two strands of dsDNA are collapsed into a duplex-family.

A group of read pairs that share the same position and UMI tags. Also referred to as a "Bag" in some metrics.

A standard file format for representing unaligned reads and their corresponding quality data.

A set of genomic intervals (or regions).

Average of all allele frequency values between 0 and 0.05, excluding loci overlapping with known germline mutations from 1000 genome data set.

A Read 1/Read 2 pair of reads from the same cluster.

The ReadCollapser program.

The read stitching program.