1.

Key Pass Filter – fails for reads that do not start with a valid 4-base ‘key’ sequence corresponding to either a library read: ‘GACT’ for Rapid Library or ‘TCAG’ for FLX Standard or a Control DNA read, ‘CATG’ (GS Junior Titanium and GS FLX Titanium chemistry; see Section 7.1 for other chemistries) (numKeyPass metric).

2.

Dots Filter – fails for reads with too many negative flows. This filter discards reads that are too short or have too many poor incorporations or interruptions. A ‘dot’ is an instance of three successive negative flows (no signal for three base flows, denoted as ‘N’). The dots filter discards reads with the last positive flow occurring at less than 83 flows (~30-50 bp) or reads with more than 5% of the flows before the last positive flow occurring as dots (numDotFailed metric).

3.

Mixed Filter – fails for reads with too many positive or ambiguous flows. This filter discards reads with too many nucleotide incorporations, possibly occurring from a bead carrying two or more DNA fragments attached, a well containing more than one DNA bead, signal contamination from a neighboring well or a low signal-to-noise ratio well. The Mixed Filter discards a read if more than 70% of the flows occurring before the last positive flow recorded a positive signal. Additionally, if the normalized flow signal value is between 0.45 and 0.75, it is considered ambiguous. If the read has more than 20% ambiguous or less than 30% unambiguous positive flows (either below 0.45 or above 0.75) the read is discarded (numMixedFailed metric).