# optimal settings found for assemblathon 1 
################################# 1
STAGE
 VERBOSE ON
PAIR_THRESHOLD 30
STRENGTH_TEST_RATIO 0.0
FIND_SIGMAS 5
MIN_UNCERTAINTY 0
EXCLUDE_SMALL_CONTIGS 3000
PREVENT_TWO_SMALL_SCAFFOLDS_JOINING 5000

# here he choose a high pair threshold, exclude a lot of small contigs, and
# turn off the strength test so that all conflicts are left unresolved.
################################# 2
STAGE
EXCLUDE_SMALL_CONTIGS 200

# perhaps we missed some joins by excluding small contigs.
################################# 3
STAGE
PAIR_THRESHOLD 15
EXCLUDE_SMALL_CONTIGS 3000

################################# 4
STAGE
EXCLUDE_SMALL_CONTIGS 500

#same again with lower threshold.
################################# 5
STAGE
PAIR_THRESHOLD 30
STRENGTH_TEST_RATIO 0.5
FIND_SIGMAS 10
EXCLUDE_SMALL_CONTIGS 3000

# now turn on strength ratio for some more aggressive stages.
################################# 6
STAGE
PAIR_THRESHOLD 15

################################# 7
STAGE
PAIR_THRESHOLD 8

################################# 8
STAGE
EXCLUDE_SMALL_CONTIGS 200

################################# 9
STAGE
STRENGTH_TEST_RATIO 0.6
# jump length can now move on to favour long-insert joins 
# that may be being blocked by erroneous short connections.

################################# 10
STAGE
PAIR_THRESHOLD 8
STRENGTH_TEST_RATIO 0.5
EXCLUDE_SMALL_CONTIGS 1000
MIN_UNCERTAINTY 300
PREVENT_TWO_SMALL_SCAFFOLDS_JOINING 3000
JUMP_LENGTH 2000

################################# 11
STAGE
PAIR_THRESHOLD 6
JUMP_LENGTH 5000

################################# 12
STAGE
JUMP_LENGTH OFF
PREVENT_TWO_SMALL_SCAFFOLDS_JOINING OFF