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 |