Autofinish

Autofinish is part of the Consed package. It automatically chooses finishing reads in order to finish a project. "Finish" is defined by you--you can have it:

Figure out how contigs are ordered and oriented
Close gaps
Improve the error rate
Cover every base by reads from at least 2 different subclones

Any of these can be turned on or off.
Autofinish will suggest any or all of the following types of reads:

Forward universal primer terminator reads
Reverse universal primer terminator reads
Custom primer reads with subclone template
Custom primer reads with whole clone template
Minilibraries
PCR

Any of these can be turned on or off.
When Autofinish has a choice of different solutions, it picks the cheapest (the cost of different types of reads can be customized).
Designed to be run in batch after Phrap runs.

Autofinish Performance

Autofinish is working very well for the labs that are using it.

The following table lists BACs that started finishing in July of 2000. As you can see, Autofinish calls all reactions for the majority of those clones. There are 7 BACs as of this writing that are not finished, and presumably those would have some human-chosen reads.

PROJECT	# FINISHING	# AUTOFINISH
	READS	READS
		(% AUTOFINISH
		READS)
djs13	237	237 (100%)
djs267	267	267 (100%)
djs510	350	326 (93%)
djs696	294	294 (100%)
djs702	206	206 (100%)
djs712	265	265 (100%)
djs701	234	234 (100%)
djs718	381	381 (100%)
djs713	170	170 (100%)
djs714	243	243 (100%)
djs715	428	428 (100%)
djs721	76	76 (100%)
djs513	128	128 (100%)
djs704	500	500 (100%)
djs709	421	421 (100%)

Why Use Autofinish?

Allows finishers to be more productive
Reduces your finishing cost
Allows most finishing to be done by production personnel
Gives finishers a more interesting and challenging job since Autofinish takes care of routine/tedious part of finishing
Much cheaper to increase your throughput using Autofinish than using more people since Autofinish has decreasing marginal cost while personnel have increasing marginal cost