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Table 5 Differences in contig connections before and after (indicating by "<" and ">" in the first column, respectively) including non-uniquely aligned contigs for (a) OMACC on E. coli data, (b) FINISH on E. coli data, (c) OMACC on GI1 data, and (d) FINISH on GI1 data.

From: OMACC: an Optical-Map-Assisted Contig Connector for improving de novo genome assembly

In Neighboring contigs Gap size (bp) Best contig path Contig path length (bp) Length difference Correct/Consistent
(a)
> 118-,032- 9331 118-:116-:032- 9334 3 1
> 060+,085+ 6070 060+:116+:085+ 7271 1201 0
(b)
> 118-,032- 9331 118-:116-:032- 9334 3 1
< 059-,107- 15847 059-:078+:063+:092+:110-:027-:107-* 15609 238 0
> 054-,118- 13029 054-:101+:084-:087-:025-:122-:123-:118- 13656 627 1
< 054-,032- 41348 054-:101+:084-:087-:025-:122-:123-:118-:116-:032- 41983 635 1
> 060+,085+ 6070 060+:116+:085+ 7271 1201 0
< 069-,108+ 113278 069-:116-:074+:082+:084-:087-:025-:122-:123-:088+:026-:092+:110-:027-:108+ 111423 1855 0
> 112+,066+ 10905 112+:116-:065+:117+:111+:066+ 14522 3617 0
> 066+,048+ 45302 066+:117+:111+:048+ 19187 26115 0
> 081+,052- 68596 081+:053-:011+:051-:052- 39775 28821 0
< 038-,076+ 144606 038-:117+:111+:075-:011-:053+:021+:124+:014-:015-:076+ 86949 57657 0
> 038-,081+ 36179 038-:117+:089-:015+:014+:124-:021-:053-:011+:068+:116+:081+ 103480 67301 0
< 085+,048+ 122463 085+:116+:007-:111-:048+ 52387 70076 0
(c)
> 014+,069+ 6852 014+:069+ 6761 91 1
< 035+,006- 67333 035+:261-:173-:099-:182+:006- 67009 324 1
< 027-,016- 75414 027-:196+:152+:196+:103-:126-:063-:016- 74985 429 1
> 048+,060- 55177 048+:175+:142-:175+:142-:175+:142-:175+:142-:175+:142-:175+:060- 55737 560 1
(d)
< 035+,006- 67333 035+:261-:173-:099-:182+:006- 67009 324 1
< 027-,016- 75414 027-:196+:103-:126-:063-:016- 72109 429 0
> 104+,074+ 35095 104+:175+:112-:167+:102+:258+:160-:136+:198-:225+:228+:074+ 37882 2787 0
> 048+,060- 55177 048+:175+:060- 34842 20335 0
> 111+,006- 25002 111+:188-:149-:115-:173-:099-:182+:006- 52888 27886 0
< 046-,119+ 23104 046-:230-:009-:154+:139-:101+:186-:105+:126-:048+:175+:053+:159-:064-:205-:227+:119+* 322943 299839 0
  1. *These contig connections are not disrupted by any non-uniquely aligned contig, but disappear when non-uniquely aligned contigs are included, indicating a bug in FINISH.