Recently , i have used two version cap3, the before version is buided at 04/15/05, the latest VersionDate is 10/15/07.
when i used the two version software to assemble the following datasets with default parameters, but, i get different result, the old version products a contigs, however, the latest result is two singletons.
So, i compare the parameters of two versions.I find, there are four different default parameters just bold line, and at the new version, three parameters (just red line)are added.
My question is that, who can tell me the three new added parameters mean ?
The another puzzle is that, i want to give the old parameter to new version, the command is "cap3 ./temp.fas -o 40 -p 80 -s 900 -y 250", but the result is also two singletons. Why?????? Is it the three new para meters to effect the assmmble???
Best regards!
old parameters(04/15/05)
-a N specify band expansion size N > 10 (20)
-b N specify base quality cutoff for differences N > 15 (20)
-c N specify base quality cutoff for clipping N > 5 (12)
-d N specify max qscore sum at differences N > 20 (200)
-e N specify clearance between no. of diff N > 10 (30)
-f N specify max gap length in any overlap N > 1 (20)
-g N specify gap penalty factor N > 0 (6)
-h N specify max overhang percent length N > 2 (20)
-m N specify match score factor N > 0 (2)
-n N specify mismatch score factor N < 0 (-5)
-o N specify overlap length cutoff > 20 (40)
-p N specify overlap percent identity cutoff N > 65 (80)
-r N specify reverse orientation value N >= 0 (1)
-s N specify overlap similarity score cutoff N > 400 (900)
-t N specify max number of word matches N > 30 (300)
-u N specify min number of constraints for correction N > 0 (3)
-v N specify min number of constraints for linking N > 0 (2)
-w N specify file name for clipping information (none)
-x N specify prefix string for output file names (cap)
-y N specify clipping range N > 5 (250)
-z N specify min no. of good reads at clip pos N > 0 (3)
new parameters(10/15/07)
-a N specify band expansion size N > 10 (20)
-b N specify base quality cutoff for differences N > 15 (20)
-c N specify base quality cutoff for clipping N > 5 (12)
-d N specify max qscore sum at differences N > 20 (200)
-e N specify clearance between no. of diff N > 10 (30)
-f N specify max gap length in any overlap N > 1 (20)
-g N specify gap penalty factor N > 0 (6)
-h N specify max overhang percent length N > 2 (20)
-i N specify segment pair score cutoff N > 20 (40)
-j N specify chain score cutoff N > 30 (80)
-k N specify end clipping flag N >= 0 (1)
-m N specify match score factor N > 0 (2)
-n N specify mismatch score factor N < 0 (-5)
-o N specify overlap length cutoff > 15 (40)
-p N specify overlap percent identity cutoff N > 65 (90)
-r N specify reverse orientation value N >= 0 (1)
-s N specify overlap similarity score cutoff N > 250 (900)
-t N specify max number of word matches N > 30 (300)
-u N specify min number of constraints for correction N > 0 (3)
-v N specify min number of constraints for linking N > 0 (2)
-w N specify file name for clipping information (none)
-x N specify prefix string for output file names (cap)
-y N specify clipping range N > 5 (100)
-z N specify min no. of good reads at clip pos N > 0 (3)
>lcl|Seq274836 No definition line found
TCAGCCGCGCAGGTATACTGACAGTGATATCACTTCCTACTAGCTAGCTGCTACTTGAAA
CTAAAGTTTTACTCTTAAGGTTCTGAAAGATTTAATAGGAACAGTATGTGGTCCTCCATA
GGATGAATTGGTTGCAATTGAGCAATAGTGTCAAAATCATCAGTTGATCAATTCTTCTGC
ATAACCATTTATGTGAAATTGACTAGAAAACAAGTTGCAAGAGAAAAATAAAGCTTTCTG
GTTTAGCTTGTTGTGTTAGCCCTTTCAGACACAGGTCAGTGTTGAACATATTTCTAAGAT
AATTAGGTTAGCTAAGATGAGAGGCAAACTCTATTTATTTGTGACCCTAAAAATGGTAGA
CTTACAAACGCCTAACTTAATCATACTCAATCTTCATGTCTACTTCAGTTAAAGAGAATA
CAATTACAACAAGTACCCAACCCGCAATCACCAATAAAAACTAAACAATCTAACAGAGAT
ATTGTTTACACTAAAGAAACAAAAACATTAAGTAAATTGACCAATGACTCCCATCGTACT
ACTGTCG
>lcl|Seq158084 No definition line found
TCAGCCGCGCAGGTATCTTCTACTACAGTGATGACATATCATTTCCATGTCTTGCAGACT
CTCTCGCATATACTGACAGTGATATCACTTCCTACTAGCTAGCTGCTACTTGAAACTAAA
GTTTTACTCTTAAGGTTCTGAAAGATTTAATAGGAACAGTATGTGATTCTCCATAGGATG
AATTGGTTGCTAATTGAGTCAAATAGTGTCAAAATCAATCAGTTGATCATTCTTCTGCAT
AACCATTTATGTAGAAATTGACTAAGAAAACAAGTTGCAAGAAGAAAAATAAAGACTTTT
ACTGGTTTAAGCTTTGTTAGTGTTAGCCCTTTACAAGACACAGGTCTAGTGTTGAACATA
TTTACTAAGATAATTAGGTTAGACTAAAGATGAGTAGCAAACTCTATTTATTGTGTACCC
AAAAATGGTAGACTTACAAACGTACCCTAATTAATCATACTCATTCTTCATGTCCTACTT
ACAAGGTTAAAGAAGTAATAACAATTACAAACTAAACGTAACCTAACCCGACAACTACAA
CCAATAAAAACTAAAAC
when i used the two version software to assemble the following datasets with default parameters, but, i get different result, the old version products a contigs, however, the latest result is two singletons.
So, i compare the parameters of two versions.I find, there are four different default parameters just bold line, and at the new version, three parameters (just red line)are added.
My question is that, who can tell me the three new added parameters mean ?
The another puzzle is that, i want to give the old parameter to new version, the command is "cap3 ./temp.fas -o 40 -p 80 -s 900 -y 250", but the result is also two singletons. Why?????? Is it the three new para meters to effect the assmmble???
Best regards!
old parameters(04/15/05)
-a N specify band expansion size N > 10 (20)
-b N specify base quality cutoff for differences N > 15 (20)
-c N specify base quality cutoff for clipping N > 5 (12)
-d N specify max qscore sum at differences N > 20 (200)
-e N specify clearance between no. of diff N > 10 (30)
-f N specify max gap length in any overlap N > 1 (20)
-g N specify gap penalty factor N > 0 (6)
-h N specify max overhang percent length N > 2 (20)
-m N specify match score factor N > 0 (2)
-n N specify mismatch score factor N < 0 (-5)
-o N specify overlap length cutoff > 20 (40)
-p N specify overlap percent identity cutoff N > 65 (80)
-r N specify reverse orientation value N >= 0 (1)
-s N specify overlap similarity score cutoff N > 400 (900)
-t N specify max number of word matches N > 30 (300)
-u N specify min number of constraints for correction N > 0 (3)
-v N specify min number of constraints for linking N > 0 (2)
-w N specify file name for clipping information (none)
-x N specify prefix string for output file names (cap)
-y N specify clipping range N > 5 (250)
-z N specify min no. of good reads at clip pos N > 0 (3)
new parameters(10/15/07)
-a N specify band expansion size N > 10 (20)
-b N specify base quality cutoff for differences N > 15 (20)
-c N specify base quality cutoff for clipping N > 5 (12)
-d N specify max qscore sum at differences N > 20 (200)
-e N specify clearance between no. of diff N > 10 (30)
-f N specify max gap length in any overlap N > 1 (20)
-g N specify gap penalty factor N > 0 (6)
-h N specify max overhang percent length N > 2 (20)
-i N specify segment pair score cutoff N > 20 (40)
-j N specify chain score cutoff N > 30 (80)
-k N specify end clipping flag N >= 0 (1)
-m N specify match score factor N > 0 (2)
-n N specify mismatch score factor N < 0 (-5)
-o N specify overlap length cutoff > 15 (40)
-p N specify overlap percent identity cutoff N > 65 (90)
-r N specify reverse orientation value N >= 0 (1)
-s N specify overlap similarity score cutoff N > 250 (900)
-t N specify max number of word matches N > 30 (300)
-u N specify min number of constraints for correction N > 0 (3)
-v N specify min number of constraints for linking N > 0 (2)
-w N specify file name for clipping information (none)
-x N specify prefix string for output file names (cap)
-y N specify clipping range N > 5 (100)
-z N specify min no. of good reads at clip pos N > 0 (3)
>lcl|Seq274836 No definition line found
TCAGCCGCGCAGGTATACTGACAGTGATATCACTTCCTACTAGCTAGCTGCTACTTGAAA
CTAAAGTTTTACTCTTAAGGTTCTGAAAGATTTAATAGGAACAGTATGTGGTCCTCCATA
GGATGAATTGGTTGCAATTGAGCAATAGTGTCAAAATCATCAGTTGATCAATTCTTCTGC
ATAACCATTTATGTGAAATTGACTAGAAAACAAGTTGCAAGAGAAAAATAAAGCTTTCTG
GTTTAGCTTGTTGTGTTAGCCCTTTCAGACACAGGTCAGTGTTGAACATATTTCTAAGAT
AATTAGGTTAGCTAAGATGAGAGGCAAACTCTATTTATTTGTGACCCTAAAAATGGTAGA
CTTACAAACGCCTAACTTAATCATACTCAATCTTCATGTCTACTTCAGTTAAAGAGAATA
CAATTACAACAAGTACCCAACCCGCAATCACCAATAAAAACTAAACAATCTAACAGAGAT
ATTGTTTACACTAAAGAAACAAAAACATTAAGTAAATTGACCAATGACTCCCATCGTACT
ACTGTCG
>lcl|Seq158084 No definition line found
TCAGCCGCGCAGGTATCTTCTACTACAGTGATGACATATCATTTCCATGTCTTGCAGACT
CTCTCGCATATACTGACAGTGATATCACTTCCTACTAGCTAGCTGCTACTTGAAACTAAA
GTTTTACTCTTAAGGTTCTGAAAGATTTAATAGGAACAGTATGTGATTCTCCATAGGATG
AATTGGTTGCTAATTGAGTCAAATAGTGTCAAAATCAATCAGTTGATCATTCTTCTGCAT
AACCATTTATGTAGAAATTGACTAAGAAAACAAGTTGCAAGAAGAAAAATAAAGACTTTT
ACTGGTTTAAGCTTTGTTAGTGTTAGCCCTTTACAAGACACAGGTCTAGTGTTGAACATA
TTTACTAAGATAATTAGGTTAGACTAAAGATGAGTAGCAAACTCTATTTATTGTGTACCC
AAAAATGGTAGACTTACAAACGTACCCTAATTAATCATACTCATTCTTCATGTCCTACTT
ACAAGGTTAAAGAAGTAATAACAATTACAAACTAAACGTAACCTAACCCGACAACTACAA
CCAATAAAAACTAAAAC
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