Table 2.
Summary of assemblies
| Budgerigar_v6.3 | PBcR | Megascaffolds from Budgerigar_v6.3 + Optical Map | Megascaffolds from PBcR + Optical Map | Illumina + 454 SOAPdenovo 2 | Zebra Finch [15] | Chicken v4 [13] * | Chicken v3 [16] | Peregrine Falcon [17] | Puerto Rican Parrot [21] | Macaw 1.1 [20] | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Assembler |
Celera CABOG [25] |
PBcR assembler [5] |
|
|
SOAPdenovo2[26] |
PCAP [27] |
NA |
PCAP [27] |
SOAPdenovo [28,29] |
Ray [30] |
CLC Genomics Workbench |
| Sequence method |
454 FLX, FLX+, Illumina |
PacBio corrected with Illumina, 454 FL×, FL×+ |
454 FLX, FLX+, Illumina, Optical Maps. |
PacBio corrected with Illumina, 454 FL×, FL×+, Optical Maps. |
Illumina, 454 FL×+ |
Sanger |
Sanger, 454 |
Sanger v2.1 |
Illumina |
Illumina |
Illumina, 454 FL×+ |
| Coverage |
14× |
17× |
|
|
137.59 Illumina, 6.85 FL×+ |
6× |
19.1× |
7.1×s |
107× |
26.9× |
26× |
| Genome size |
1.2Gbp |
1.2Gbp |
1.2Gbp |
1.2Gbp |
1.2Gbp |
1.2Gbp |
1.2Gbp |
1.05Gbp |
1.2Gbp |
1.58Gbp |
1.2 Gbp |
| Total bases in scaffolds |
1,117,358,947 |
1,219,132,003 |
1,118,758,630 |
1,241,439,339 |
1,169,860,945 |
1,224,525,252 |
1,046,932,099 |
1,047,124,295 |
1,174,046,505 |
1,164,566,833 |
997,000 |
| Number of scaffolds |
25,212 |
54,668 |
25,163 |
54,138 |
151,393 |
37,698 |
15,932 |
23,776 |
21,224 |
148,255 |
140,453 |
| Avg. scaffold size |
44,319 |
22,300 |
44,460 |
22,931 |
7,727 |
32,482 |
65,713 |
44,041 |
55,317 |
7,855 |
Not available |
| N50 scaffold size |
10,614,387 |
1,705,751 |
13,823,040 |
7,280,340 |
13,497,021 |
10,409,499 |
90,216,835 |
11,125,310 |
3,891,469 |
19,470 |
15,968 |
| Largest scaffold size |
39,887,647 |
11,564,683 |
61,483,320 |
33,208,800 |
66,566,439 |
56,620,707 |
195,276,750 |
51,053,708 |
18,327,016 |
206,462 |
177,843 |
| Total gaps in scaffolds |
51,150 |
26,444 |
51,295# |
27,118 |
60810 |
124,736 |
NA |
NA |
77,368 |
Not available |
Not available |
| Number of Contigs |
70,863 |
77,556 |
NA |
NA |
212,203 |
126,053 |
27,027 |
85,191 |
98,540 |
259,423 |
214,754* |
| Avg. contig size |
15,334 |
15,344 |
NA |
NA |
4664 |
9,714 |
38,736 |
12,291 |
11,914 |
4,304 |
Not available |
| N50 contig size |
55,633 |
102,885 |
NA |
NA |
51,034 |
38,549 |
279,750 |
45,280 |
28,599 |
6,983 |
6,366 |
| Largest contig size | 465,633 | 849,044 | NA | NA | 500,974 | 424,635 | NA | 624,663 | 247,807 | 75,003 | 87,225 |
*The Chicken v4 assembly consists of chromosomes and not scaffolds with explains the very high scaffold length statistics.
#The increased number of gaps in megascaffolds reflects the fact that each megascaffold may be merger of many original scaffolds with gaps in between them.