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scafsettings.txt
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scafsettings.txt
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# optimal settings found for GAGE human chromasome data
################################# 1
STAGE
VERBOSE ON
PAIR_THRESHOLD MIN_EDGE
STRENGTH_TEST_RATIO 0.0
FIND_SIGMAS NUM_SIGMA
MIN_UNCERTAINTY 0
EXCLUDE_SMALL_CONTIGS MIN_LEN
PREVENT_TWO_SMALL_SCAFFOLDS_JOINING MIN_LEN
# 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.
################################# 4
STAGE
PAIR_THRESHOLD 5
STRENGTH_TEST_RATIO 0.5
EXCLUDE_SMALL_CONTIGS 6000
################################# 6
STAGE
PAIR_THRESHOLD 10
STRENGTH_TEST_RATIO 0.6
################################# 7
STAGE
PAIR_THRESHOLD 10
STRENGTH_TEST_RATIO 0.7
EXCLUDE_SMALL_CONTIGS 500
################################# 11
STAGE
PAIR_THRESHOLD 10
PREVENT_TWO_SMALL_SCAFFOLDS_JOINING 2000
JUMP_LENGTH 6000
################################# 11
STAGE
PAIR_THRESHOLD 10
PREVENT_TWO_SMALL_SCAFFOLDS_JOINING 2000
JUMP_LENGTH 8000
################################# 11
STAGE
PAIR_THRESHOLD 10
PREVENT_TWO_SMALL_SCAFFOLDS_JOINING 2000
JUMP_LENGTH 10000
################################# 11
STAGE
PAIR_THRESHOLD 10
PREVENT_TWO_SMALL_SCAFFOLDS_JOINING 2000
JUMP_LENGTH 15000
################################# 11
STAGE
PAIR_THRESHOLD 10
PREVENT_TWO_SMALL_SCAFFOLDS_JOINING 2000
JUMP_LENGTH 25000
################################# 11
STAGE
PAIR_THRESHOLD 10
PREVENT_TWO_SMALL_SCAFFOLDS_JOINING 2000
JUMP_LENGTH 35000
################################# 11
STAGE
PAIR_THRESHOLD 10
PREVENT_TWO_SMALL_SCAFFOLDS_JOINING 2000
JUMP_LENGTH 45000