Version Differences for HGAP

==Discard Unconvincing Contigs==

We aligned subreads to contigs, and discarded the contigs with fewer than 100 reads aligned.

-

===Performance===

+

==Performance==

{| {{table}} border="1"

| align="center" style="background:#f0f0f0;"|'''Statistics without reference '''

-

| align="center" style="background:#f0f0f0;"|'''All Data'''

| align="center" style="background:#f0f0f0;"|'''4 SMRT cells : 1st Set'''

| align="center" style="background:#f0f0f0;"|'''4 SMRT cells : 2nd Set'''

| align="center" style="background:#f0f0f0;"|'''6 SMRT cells : 2nd Set'''

| align="center" style="background:#f0f0f0;"|'''6 SMRT cells : 3rd Set'''

+

| align="center" style="background:#f0f0f0;"|'''8 SMRT cells : 1st Set'''

+

| align="center" style="background:#f0f0f0;"|'''8 SMRT cells : 2nd Set'''

+

| align="center" style="background:#f0f0f0;"|'''8 SMRT cells : 3rd Set'''

|-

-

|# contigs||7||8||10||12||4||9||12

+

|# contigs||5||10||4||11||7||8||6||10||5

|-

-

|Largest contig||2 198 457||3 4848 77||1 936 831||1 948 632||2 104 087||1 169 224||1 439 551

+

|Largest contig||3 770 578||4 106 852||4 644 754||3 785 116||4 647 724||3 287 965||4 649 322||4 623 068||4 649 308

|-

-

|Total length||4 706 061||4 674 582||4 659 277||4 682 754||4 680 475||4 702 993||4 739 366

+

|Total length||4 684 069||4 723 363||4 671 153||4 736 342||4 711 060||4 708 831||4 706 433||4 731 334||4 691 736

|-

-

|N50||1 005 770 ||3 484 877||966 809||1 434 284||1 655 500||676 526||1 268 010

+

|N50||3 770 578||4 106 852||4 644 754||3 785 116||4 647 724||3 287 965||4 649 322||4 623 068||4 649 308

|-

| style="background:#f0f0f0;"| '''Misassemblies'''||||||||||||||

-

|# misassemblies||10||7||8||9||9||8||10

+

|# misassemblies||10||13||13||15||12||11||11||16||12

|-

-

|Misassembled contigs length ||2 836 368||3 498 134||2 903 640||3 591 179||3 759 587||2 275 404||3 975 983

+

|Misassembled contigs length ||3 788 648||4 700 016||4 671 153||4 726 005||4 685 712||3 339 030||4 694 303||4 698 068||4 649 308

|-

| style="background:#f0f0f0;"| '''Mismatches'''||||||||||||||

-

|# mismatches per 100kbp||0.8||0.43||0.45||1.27||0.15||0.75||0.58

+

|# mismatches per 100kbp||0.47||0.56||0.37||0.19||0.11||0.15||0.13||0.43||0.17

|-

-

|# indels per 100kbp||5.71||2.98||3.56||8.72||1.77||6.06||6.88

+

|# indels per 100kbp||1.08||4.44||0.22||1.66||0.63||0.65||0.19||4.59||0.56

|-

-

|# N's per 100kbp ||0||0||0||0||0||0||0

+

|# N's per 100kbp ||0||0||0||0||0||0||0||0||0

|-

| style="background:#f0f0f0;"| '''Genome Statistics'''||||||||||||||

-

|Genome fraction(%) ||100||100||99.798||99.87||100||99.995||99.979

+

|Genome fraction(%) ||100||100||99.994||99.999||100||100||100||99.99||100

|-

-

|Duplication ratio ||1.014||1.009||1.006||1.012||1.009||1.014||1.023

+

|Duplication ratio ||1.01||1.018||1.007||1.021||1.031||1.015||1.012||1.02||1.011

|-

-

|# genes ||4494+3 part||4494+3 part||4479+8 part||4485+9 part||4494+3 part||4493+4 part||4492+5 part

+

|# genes ||4495+2 part||4495+2 part||4493+3 part||4494+3 part||4495+2 part||4495+2 part||4495+2 part||4494+3 part||4495+2 part

|-

-

|NGA50 ||615 234||1 205 052||572 342||875 953||844 482||633 220||1 267 242

+

|NGA50 ||1 207 217||2 558 505||1 640 882||2 888 022||2 834 458||1 298 912||1 477 605||1 344 200||2 995 586

-

|-

+

|-

|}

 ==Discard Unconvincing Contigs==
 We aligned subreads to contigs, and discarded the contigs with fewer than 100 reads aligned.
-								===Performance===
+								==Performance==
 {| {{table}} border="1"
 | align="center" style="background:#f0f0f0;"|'''Statistics without reference '''
-								| align="center" style="background:#f0f0f0;"|'''All Data'''
 | align="center" style="background:#f0f0f0;"|'''4 SMRT cells : 1st Set'''
 | align="center" style="background:#f0f0f0;"|'''4 SMRT cells : 2nd Set'''
 | align="center" style="background:#f0f0f0;"|'''6 SMRT cells : 2nd Set'''
 | align="center" style="background:#f0f0f0;"|'''6 SMRT cells : 3rd Set'''
 								| align="center" style="background:#f0f0f0;"|'''8 SMRT cells : 1st Set'''
 								| align="center" style="background:#f0f0f0;"|'''8 SMRT cells : 2nd Set'''
 								| align="center" style="background:#f0f0f0;"|'''8 SMRT cells : 3rd Set'''
 |-
-								|# contigs||7||8||10||12||4||9||12
+								|# contigs||5||10||4||11||7||8||6||10||5
 |-
-								|Largest contig||2 198 457||3 4848 77||1 936 831||1 948 632||2 104 087||1 169 224||1 439 551
+								|Largest contig||3 770 578||4 106 852||4 644 754||3 785 116||4 647 724||3 287 965||4 649 322||4 623 068||4 649 308
 |-
-								|Total length||4 706 061||4 674 582||4 659 277||4 682 754||4 680 475||4 702 993||4 739 366
+								|Total length||4 684 069||4 723 363||4 671 153||4 736 342||4 711 060||4 708 831||4 706 433||4 731 334||4 691 736
 |-
-								|N50||1 005 770 ||3 484 877||966 809||1 434 284||1 655 500||676 526||1 268 010
+								|N50||3 770 578||4 106 852||4 644 754||3 785 116||4 647 724||3 287 965||4 649 322||4 623 068||4 649 308
 |-
 | style="background:#f0f0f0;"| '''Misassemblies'''||||||||||||||
-								|# misassemblies||10||7||8||9||9||8||10
+								|# misassemblies||10||13||13||15||12||11||11||16||12
 |-
-								|Misassembled contigs length ||2 836 368||3 498 134||2 903 640||3 591 179||3 759 587||2 275 404||3 975 983
+								|Misassembled contigs length ||3 788 648||4 700 016||4 671 153||4 726 005||4 685 712||3 339 030||4 694 303||4 698 068||4 649 308
 |-
 | style="background:#f0f0f0;"| '''Mismatches'''||||||||||||||
-								|# mismatches per 100kbp||0.8||0.43||0.45||1.27||0.15||0.75||0.58
+								|# mismatches per 100kbp||0.47||0.56||0.37||0.19||0.11||0.15||0.13||0.43||0.17
 |-
-								|# indels per 100kbp||5.71||2.98||3.56||8.72||1.77||6.06||6.88
+								|# indels per 100kbp||1.08||4.44||0.22||1.66||0.63||0.65||0.19||4.59||0.56
 |-
-								|# N's per 100kbp ||0||0||0||0||0||0||0
+								|# N's per 100kbp ||0||0||0||0||0||0||0||0||0
 |-
 | style="background:#f0f0f0;"| '''Genome Statistics'''||||||||||||||
-								|Genome fraction(%) ||100||100||99.798||99.87||100||99.995||99.979
+								|Genome fraction(%) ||100||100||99.994||99.999||100||100||100||99.99||100
 |-
-								|Duplication ratio ||1.014||1.009||1.006||1.012||1.009||1.014||1.023
+								|Duplication ratio ||1.01||1.018||1.007||1.021||1.031||1.015||1.012||1.02||1.011
 |-
-								|# genes ||4494+3 part||4494+3 part||4479+8 part||4485+9 part||4494+3 part||4493+4 part||4492+5 part
+								|# genes ||4495+2 part||4495+2 part||4493+3 part||4494+3 part||4495+2 part||4495+2 part||4495+2 part||4494+3 part||4495+2 part
 |-
-								|NGA50 ||615 234||1 205 052||572 342||875 953||844 482||633 220||1 267 242
+								|NGA50 ||1 207 217||2 558 505||1 640 882||2 888 022||2 834 458||1 298 912||1 477 605||1 344 200||2 995 586
 								|-
 |}