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 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%)
|
- 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