High-coverage sequencing and annotated assemblies of the budgerigar genome

Ganapathy, Ganeshkumar; Howard, Jason T; Ward, James M; Li, Jianwen; Li, Bo; Li, Yingrui; Xiong, Yingqi; Zhang, Yong; Zhou, Shiguo; Schwartz, David C; Schatz, Michael; Aboukhalil, Robert; Fedrigo, Olivier; Bukovnik, Lisa; Wang, Ty; Wray, Greg; Rasolonjatovo, Isabelle; Winer, Roger; Knight, James R; Koren, Sergey; Warren, Wesley C; Zhang, Guojie; Phillippy, Adam M; Jarvis, Erich D

doi:10.1186/2047-217X-3-11

GigaScience

Table 2 Summary of assemblies

From: High-coverage sequencing and annotated assemblies of the budgerigar genome

	Budgerigar_v6.3	PBcR	Megascaffolds from Budgerigar_v6.3 + Optical Map	Megascaffolds from PBcR + Optical Map	Illumina + 454 SOAPdenovo2	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.

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ISSN: 2047-217X

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