Comparative genomic data of the Avian Phylogenomics Project.

BACKGROUND: The evolutionary relationships of modern birds are among the most challenging to understand in systematic biology and have been debated for centuries. To address this challenge, we assembled or collected the genomes of 48 avian species spanning most orders of birds, including all Neognathae and two of the five Palaeognathae orders, and used the genomes to construct a genome-scale avian phylogenetic tree and perform comparative genomics analyses (Jarvis et al. in press; Zhang et al. in press). Here we release assemblies and datasets associated with the comparative genome analyses, which include 38 newly sequenced avian genomes plus previously released or simultaneously released genomes of Chicken, Zebra finch, Turkey, Pigeon, Peregrine falcon, Duck, Budgerigar, Adelie penguin, Emperor penguin and the Medium Ground Finch. We hope that this resource will serve future efforts in phylogenomics and comparative genomics.
FINDINGS: The 38 bird genomes were sequenced using the Illumina HiSeq 2000 platform and assembled using a whole genome shotgun strategy. The 48 genomes were categorized into two groups according to the N50 scaffold size of the assemblies: a high depth group comprising 23 species sequenced at high coverage (>50X) with multiple insert size libraries resulting in N50 scaffold sizes greater than 1 Mb (except the White-throated Tinamou and Bald Eagle); and a low depth group comprising 25 species sequenced at a low coverage (~30X) with two insert size libraries resulting in an average N50 scaffold size of about 50 kb. Repetitive elements comprised 4%-22% of the bird genomes. The assembled scaffolds allowed the homology-based annotation of 13,000 ~ 17000 protein coding genes in each avian genome relative to chicken, zebra finch and human, as well as comparative and sequence conservation analyses.
CONCLUSIONS: Here we release full genome assemblies of 38 newly sequenced avian species, link genome assembly downloads for the 7 of the remaining 10 species, and provide a guideline of genomic data that has been generated and used in our Avian Phylogenomics Project. To the best of our knowledge, the Avian Phylogenomics Project is the biggest vertebrate comparative genomics project to date. The genomic data presented here is expected to accelerate further analyses in many fields, including phylogenetics, comparative genomics, evolution, neurobiology, development biology, and other related areas.

Data description

Here we presented the genomes of 48 bird species, representing 36 orders of birds, including all Neognathae and two of the five Palaeognathae orders, collected by the Avian Genome Consortium ( [1], full author list of the Consortium provided in Additional file 1 and data in GigaDB [2]). The Chicken, Zebra finch, and Turkey genomes (sequenced using the Sanger method) were collected from the public domain. Another three genomes, the Pigeon, Peregrine Falcon and Duck, have been published during the development of this project [3-5], and five genomes, the Budgerigar, Crested Ibis, Little Egret, Emperor and Adele penguins, are reported in companion studies of this project [6, 7]. The data downloads for the remaining 38 genomes are released here.

Genome sequencing

Tissue samples were collected from multiple sources, with the largest contributions from the Copenhagen Zoo (Denmark) and the Louisiana State University (USA). Most DNA samples were processed and quality control performed at the University of Copenhagen (Dr. Gilbert’s lab, Denmark) and Duke University (Dr. Jarvis’ lab, USA). The collected samples were then used for constructing pair-end libraries and sequenced using Illumina HiSeq 2000 platforms at the BGI (China). For the high-coverage birds, multiple pair-end libraries with a series of up to 9 insert sizes (170 bp, 500 bp, 800 bp, 2 kb, 5 kb, 10 kb and 20 kb) were constructed for each species, as part the first 100 species of the G10K project. For four birds (Anas platyrhynchos, Picoides pubescens, Ophisthocomus hoazin and Tinamus guttatus), libraries of some insert sizes were not constructed due to limited sample amounts or the sequencing strategies applied to those species. In addition, for the budgerigar genome, Roche 454 longer reads of multiple insert sizes were used [6]. For the low-coverage genomes, libraries of two insert sizes (500 bp and 800 bp) were constructed. The sequencing depths for high-coverage genomes were 50X to 160X, whereas the sequencing depths for low-coverage genomes were 24X to 39X. An effort was made to obtain DNA samples from tissues with associated museum voucher specimens with high quality metadata.

Genome assembly

Before assembly, several quality control steps were performed to filter the low-quality raw reads. The clean reads of each bird were then passed to SOAPdenovo v1.05 [8] for de novo genome assembly. We tried different k-mers (from 23-mer to 33-mer) to construct contigs and chose the k-mer with the largest N50 contig length. In addition, we also tried different cut-offs of read pairs for different libraries to link contigs into scaffolds. The assembly with the largest N50 length was finally used.

All the assemblies have similar genome sizes, ranging from 1.04-1.26Gb (Table  1). The high-coverage genomes have a N50 scaffold length of >1 Mb, except for the White-throated Tinamou (Tinamous guttatus) with a scaffold N50 of 242 Kb and Bald Eagle (Haliaeetus leucocephalus) with a scaffold N50 of 670 Kb, due to no 10 kb and 20 kb libraries for these two genomes. For low-coverage genomes, the scaffold N50 lengths ranged from 30 kb to 64 kb. The N50 contig lengths for high-coverage genomes were from 19 kb to 55 kb, and the low coverage genomes were from 12 kb to 20 kb. The Parrot and Ostrich genomes were further assembled with the aid of optical mapping data, thus achieving much larger scaffold N50 sizes.

Table 1

Basic statistics for the assemblies of avian species

Species	Common name	Sequencing depth	Library	Assembly (contig/scaffold N50;total length)
Published (Sanger sequencing)
Gallus gallus	Chicken	7X	-	36 K/7.07 M;1.05G
Taeniopygia guttata	Zebra finch	6X	-	39 K/10 M;1.2G
Meleagris gallopavo	Turkey	17X	-	12.6 K/1.5 M;1.04G
High - coverage genomes
Anas platyrhynchos domestica	Peking duck	50X	200,500,2 k,5 k,10 k	26 K/1.2 M;1.1G
Columba livia	Pigeon	63X	200,500,800,2 k,5 k,10 k,20 k	22 K/3.2 M;1.11G
Falco peregrinus	Peregrine falcon	105X	200,500,800,2 k,5 k,10 k,20 k	28 K/3.9 M;1.18G
Pygoscelis adeliae	Adelie penguin	60X	200,500,800,2 k,5 k,10 k,20 k	19 K/5.0 M;1.23G
Aptenodytes forsteri	Emperor penguin	60X	200,500,2 k,5 k,10 k,20 k	30 K/5.1 M;1.26G
Nipponia nippon	Crested ibis	105X	200,500,800,2 k,5 k,10 k,20 k	22 K/5.4 M;1.17G
Egretta garzetta	Little egret	74X	200,500,800,2 k,5 k,10 k,20 k	24 K/3.1 M;1.2G
Calypte anna	Anna's hummingbird	110X	200,500,800,2 k,5 k,10 k,20 k	23 K/4 M;1.1G
Chaetura pelagica	Chimney swift	103X	200,500,800,2 k,5 k,10 k,20 k	27 K/3.8 M;1.1G
Charadrius vociferus	Killdeer	100X	200,500,800,2 k,5 k,10 k,20 k	32 K/3.6 M;1.2G
Cuculus canorus	Common cuckoo	100X	200,500,800,2 k,5 k,10 k,20 k	31 K/3 M;1.15G
Ophisthocomus hoazin	Hoatzin	100X	200,500,800,2 k,5 k,10 k	24 K/2.9 M;1.14G
Geospiza fortis	Medium ground finch	115X	200,500,800,2 k,5 k,10 k,20 k	30 K/5.2 M;1.07G
Manacus vitellinus	Golden-collared manakin	110X	200,500,800,2 k,5 k,10 k,20 k	34 K/2.5 M;1.12G
Melopsittacus undulatus	Budgerigar	160X	200, 500, 800, 2 k, 5 k, 10 k	55 K/10.6 M;1.1G
Picoides pubescens	Downy woodpecker	105X	200,500,800,2 k,5 k,10 k	20 K/2 M;1.17G
Struthio camelus	Ostrich	85X	200,500,800,2 k,5 k,10 k,20 k	29 K/3.5 M;1.23G
Tinamus guttatus	White-throated tinamou	100X	200,500,800,2 k,5 k	24 K/242 K;1.05G
Corvus brachyrhynchos	American crow	80X	200,500,800,2 k,5 k,10 k,20 k	24 K/6.9 M;1.1G
Haliaeetus leucocephalus	Bald eagle	88X	300,400,3 k,8 k	10 K/670 K;1.26G
Low - coverage genomes
Antrostomus carolinensis	Chuck-will's-widow	30X	500, 800	17 K/45 K;1.15G
Cariama cristata	Red-legged seriema	24X	500, 800	17 K/54 K;1.15G
Colius striatus	Speckled mousebird	27X	500, 800	18 K/45 k;1.08G
Merops nubicus	Carmine bee-eater	37X	500, 800	20 K/47 K;1.06G
Gavia stellata	Red-throated loon	33X	500, 800	16 K/45 K;1.15G
Balearica regulorum	Grey-crowned crane	33X	500, 800	18 K/51 K;1.14G
Apaloderma vittatum	Bar-tailed trogon	28X	500, 800	19 K/56 K;1.08G
Phalacrocorax carbo	Great cormorant	24X	500, 800	15 K/48 K;1.15G
Phaethon lepturus	White-tailed tropicbird	39X	500, 800	18 K/47 K;1.16G
Phoenicopterus ruber ruber	American flamingo	33X	500, 800	16 K/37 K;1.14G
Podiceps cristatus	Great-crested grebe	30X	500, 800	13 K/30 K;1.15G
Fulmarus glacialis	Northern fulmar	33X	500, 800	17 K/46 K;1.14G
Tyto alba	Barn owl	27X	500, 800	13 K/51 K;1.14G
Tauraco erythrolophus	Red-crested turaco	30X	500, 800	18 K/55 K;1.17G
Cathartes aura	Turkey vulture	25X	500, 800	12 K/35 K;1.17G
Eurypyga helias	Sunbittern	33X	500, 800	16 K/46 K;1.1G
Mesitornis unicolor	Brown mesite	29X	500, 800	18 K/46 K;1.1G
Leptosomus discolor	Cuckoo-roller	32X	200, 500, 800	19 K/61 K;1.15G
Chlamydotis macqueenii	MacQueen's Bustard	27X	500, 800	18 K/45 K;1.09G
Pelecanus crispus	Dalmatian pelican	34X	500, 800	18 K/43 K;1.17G
Pterocles gutturalis	Yellow-thoated sandgrouse	25X	500, 800	17 K/49 K;1.07G
Acanthisitta chloris	Rifleman	29X	500, 800	18 K/64 K;1.05G
Buceros rhinoceros	Rhinoceros hornbill	35X	500, 800	14 K/51 K;1.08G
Nestor notabilis	Kea	32X	500, 800	16 K/37 K;1.14G
Haliaeetus albicilla	White-tailed eagle	26X	500, 800	20 K/56 K;1.14G

Repeat annotation

RepeatMasker [9] and RepeatModeler [10] were used to perform repeat annotations for the bird genomes. The overall annotated content of transposable elements (TE) range from within 2-9% of all bird genomes except Woodpecker (Table  2). These TEs include long interspersed nuclear elements [LINEs], short interspersed nuclear elements [SINEs], long-terminal repeat [LTR] elements and DNA transposons). The exception Woodpecker genome has a TE content of 22%, which reflects a larger number of LINE CR1 elements (18% of the genome).

Table 2

Percentages of genome annotated as transposable elements (TEs)

Species	LINE	SINE	LTR	DNA	RC	Unknown	Total
Merops nubicus	5.01	0.07	1.30	0.14	0.01	1.26	7.78
Picoides pubescens	18.20	0.05	0.89	0.17	0.00	2.84	22.15
Buceros rhinoceros	3.62	0.08	1.05	0.16	0.01	1.09	6.00
Apaloderma vittatum	5.97	0.12	1.31	0.23	0.01	0.82	8.44
Leptosomus discolor	2.93	0.12	1.32	0.19	0.01	1.88	6.45
Colius striatus	6.54	0.10	2.19	0.19	0.00	0.39	9.42
Haliaeetus albicilla	2.55	0.14	1.71	0.19	0.01	0.77	5.37
Haliaeetus leucocephalus	2.01	0.17	1.89	0.22	0.00	2.59	6.89
Cathartes aura	2.21	0.17	1.05	0.19	0.00	0.92	4.54
Tyto alba	2.64	0.13	1.79	0.19	0.01	0.74	5.49
Geospiza fortis	3.65	0.06	3.37	0.31	0.04	0.80	8.23
Taeniopygia guttata	3.79	0.06	4.11	0.32	0.02	1.39	9.68
Corvus brachyrhynchos	3.73	0.07	2.43	0.22	0.02	0.90	7.37
Manacus vitellinus	4.43	0.08	1.08	0.25	0.01	0.72	6.58
Acanthisitta chloris	6.38	0.10	1.46	0.21	0.01	0.56	8.72
Melopsittacus undulatus	6.49	0.08	1.97	0.20	0.01	0.45	9.19
Nestor notabilis	4.60	0.10	1.32	0.18	0.00	0.37	6.57
Falco peregrinus	3.09	0.15	1.27	0.28	0.00	0.71	5.50
Cariama cristata	3.51	0.18	0.91	0.20	0.00	0.69	5.49
Egretta garzetta	3.92	0.12	1.42	0.24	0.01	1.22	6.93
Pelecanus crispus	3.94	0.15	1.87	0.21	0.01	1.27	7.45
Nipponia nippon	3.69	0.13	1.22	0.29	0.01	0.83	6.16
Phalacrocorax carbo	3.95	0.16	1.29	0.21	0.00	0.62	6.23
Aptenodytes forsteri	2.41	0.20	1.17	0.26	0.00	1.46	5.50
Pygoscelis adeliae	3.31	0.20	1.32	0.26	0.00	0.95	6.04
Fulmarus glacialis	2.86	0.18	1.19	0.22	0.01	0.87	5.32
Gavia stellata	3.17	0.14	0.71	0.22	0.01	0.85	5.09
Eurypyga helias	4.61	0.10	1.60	0.15	0.00	0.46	6.92
Phaethon lepturus	3.91	0.12	1.71	0.22	0.00	1.48	7.44
Ophisthocomus hoazin	4.69	0.11	1.30	0.16	0.01	1.63	7.90
Balearica regulorum	3.35	0.14	1.51	0.24	0.01	0.83	6.08
Charadrius vociferus	4.53	0.13	1.12	0.20	0.01	1.05	7.03
Calypte anna	5.62	0.07	1.23	0.21	0.01	0.91	8.05
Chaetura pelagica	5.28	0.11	0.90	0.19	0.00	2.57	9.05
Antrostomus carolinensis	5.40	0.12	1.84	0.33	0.02	0.53	8.24
Chlamydotis macqueenii	3.97	0.17	1.40	0.23	0.00	0.57	6.35
Tauraco erythrolophus	2.76	0.09	1.80	0.16	0.01	3.83	8.64
Cuculus canorus	7.84	0.08	0.67	0.27	0.01	0.58	9.45
Mesitornis unicolor	4.62	0.09	1.38	0.38	0.01	1.03	7.51
Pterocles gutturalis	3.46	0.09	1.36	0.17	0.01	0.67	5.75
Columba livia	4.18	0.09	0.76	0.35	0.01	1.87	7.25
Phoenicopterus ruber	2.69	0.15	1.04	0.23	0.01	1.49	5.60
Podiceps cristatus	4.80	0.10	1.60	0.20	0.01	0.60	7.31
Gallus gallus	6.01	0.08	1.65	1.01	0.01	1.07	9.82
Meleagris gallopavo	5.40	0.05	1.11	0.82	0.00	0.52	7.90
Anas platyrhynchos	4.05	0.10	1.10	0.20	0.01	0.39	5.85
Struthio camelus	2.88	0.18	0.17	0.36	0.01	0.90	4.49
Tinamus guttatus	2.73	0.09	0.30	0.33	0.01	0.65	4.11

Protein-coding gene annotation

We used the homology-based method to annotate genes, with gene sets of chicken, zebra finch and human in Ensembl release 60 [11]. Because the quality of homology-based prediction strongly depends on the quality of the reference gene sets, we carefully chose the reference genes for the annotation pipeline. The protein sequences of these three species were compiled and used as a reference gene set template for homology-based gene predictions for the newly assembled bird genomes. We aligned protein sequences of the reference gene set to each genome by TBLASTN and used Genewise [12] to predict gene models in the genomes. A full description of the homology-based annotations is in our comparative genomics paper [1]. All the avian genomes have similar coding DNA sequence (CDS), exon, and intron lengths (Table  3).

Table 3

Statistics of protein-coding gene annotations of all the birds

Species	Gene number	Mean gene length (kb)	Mean CDS length (bp)	Mean exon length (bp)	Mean intron length (bp)	Mean intergenic length (kb)
Acanthisitta chloris	14596	13.5	1242	158.6	1800	12
Anas platyrhynchos domestica	16521	17.8	1317	160.7	2298	42
Antrostomus carolinensis	14676	12.0	1177	164.1	1747	12
Apaloderma vittatum	13615	13.5	1247	160.8	1806	12
Aptenodytes forsteri	16070	20.9	1397	161.6	2546	56
Balearica regulorum	14173	13.8	1276	162.7	1828	11
Buceros rhinoceros	13873	13.5	1267	160.4	1767	11
Calypte anna	16000	18.5	1386	161.7	2264	47
Cariama cristata	14216	13.7	1249	161.8	1849	11
Cathartes aura	13534	10.8	1109	166.4	1716	10
Chaetura pelagica	15373	19.8	1411	161.0	2364	51
Charadrius vociferus	16860	19.1	1324	161.8	2482	52
Chlamydotis macqueenii	13582	12.9	1257	162.9	1734	10
Colius striatus	13538	12.4	1190	161.1	1754	11
Columba livia	16652	18.3	1363	161.0	2277	46
Corvus brachyrhynchos	16562	17.9	1363	161.1	2220	48
Cuculus canorus	15889	20.0	1400	160.7	2413	48
Egretta garzetta	16585	18.6	1274	160.7	2496	52
Eurypyga helias	13974	12.3	1193	163.9	1763	11
Falco peregrinus	16242	19.9	1403	160.7	2389	49
Fulmarus glacialis	14306	12.8	1230	163.0	1765	11
Gallus gallus	16516	21.1	1433	158.1	2437	48
Gavia stellata	13454	13.2	1250	162.1	1776	11
Geospiza fortis	16286	17.9	1362	160.1	2198	46
Haliaeetus albicilla	13831	14.2	1258	161.1	1903	12
Haliaeetus leucocephalus	16526	19.0	1359	160.7	2370	36
Leptosomus discolor	14831	13.9	1236	163.2	1926	14
Manacus vitellinus	15285	18.8	1392	159.7	2262	46
Meleagris gallopavo	16051	17.4	1305	158.0	2215	52
Melopsittacus undulatus	15470	19.8	1395	162.2	2415	52
Merops nubicus	13467	13.0	1224	162.1	1798	11
Mesitornis unicolor	15371	11.4	1169	163.6	1666	11
Nestor notabilis	14074	14.4	1307	160.1	1822	12
Nipponia nippon	16756	19.4	1358	161.2	2434	51
Ophisthocomus hoazin	15702	20.0	1336	162.1	2582	55
Pelecanus crispus	14813	11.9	1183	164.8	1740	11
Phaethon lepturus	14970	12.7	1220	163.9	1781	11
Phalacrocorax carbo	13479	13.5	1258	162.0	1810	11
Phoenicopterus ruber	14024	11.7	1179	165.3	1716	10
Picoides pubescens	15576	20.0	1390	161.7	2450	47
Podiceps cristatus	13913	10.4	1137	165.8	1583	8
Pterocles gutturalis	13867	12.8	1235	162.5	1757	11
Pygoscelis adeliae	15270	21.3	1392	160.3	2589	58
Struthio camelus	16178	19.5	1289	161.0	2601	54
Taeniopygia guttata	17471	21.4	1383	153.5	2493	53
Tauraco erythrolophus	15435	13.2	1200	164.0	1894	12
Tinamus guttatus	15788	14.7	1288	162.0	1934	25
Tyto alba	13613	13.8	1240	160.8	1871	12

Syntenic-based orthlogous annotation

To obtain more accurate orthology annotations for phylogenetic analyses in [13], we re-annotated some genes of the Chicken and Zebra Finch based on synteny, thereby correcting errors in the annotations due to being annotated independently with different methods. We first ran bi-directional BLAST to recognize the reciprocal best hits (considered as pairwise orthologs) between our re-annotated chicken genome and each of the other genomes. Then we identified syntenic blocks by using pairwise orthologs as anchors. We only kept the pairwise orthologs with syntenic support. In addition, we also considered the genomic syntenic information inferred from the LASTZ genome alignments, and removed pairwise orthologs without genomic syntenic support. After the above filtering, all the remaining pairwise orthologs were combined into a merged list by using a chicken gene set as a reference. We also required each orthologous group to have members in at least 42 out of 48 avian species. Ultimately, we obtained a list of 8295 syntenic-based orthologs. We used the same methods to generate 12815 syntenic-based orthologs of 24 mammalian species. A full description of the synteny-based annotations is found in our phylogenomics paper [13].

Sequence alignments

Protein coding gene alignment

CDS alignments for all orthologous genes were obtained by two rounds of alignments. In order to preserve the reading frames of CDS, we aligned the amino acid sequences and then back translated them into DNA alignments. In the first round of alignment, SATé-Prank [14] was employed to obtain the initial alignments, which were used to identify the aberrant over-aligned and under-aligned sequences. The aberrant sequences were then removed, and the second round of alignment were performed by SATé-MAFFT [14] for the filtered sequences to create the final multiple sequence alignments. The default JTT model inside SATé [14] was used as we found it to fit the data best for most genes. We also used the same method to generate the alignments of mammalian orthologs. More details of the alignment are presented in Jarvis et al. [13].

Whole genome alignment

Whole genome alignments are very useful for comparative analyses, so we generated a multiple genome alignment of all 48 bird species. Firstly, pairwise alignments for each two genomes (with repeats masked) were produced by LASTZ [15], using chicken as the reference genome. Next chainNet [16] was introduced to obtain improved pairwise alignments. Finally, we used MULTIZ [17] to merge the pairwise alignments into multiple genome alignments. Approximately 400 Mb of each avian genome made it into the final alignment result. Thereafter, the alignment was filtered for over- and under-aligned errors, and for presence in 42 of 48 avian species. The resultant alignment was about 322 Mb, representing about one third of each genome, suggesting a large portion of the genome has been under strong constraints after different bird species diverged from their common ancestor. More details of the alignment are presented in Jarvis et al. [13].

dN/dS estimates

We deposit dN/dS estimates (ratio of non-synonymous versus synonymous substitution rates) of the protein coding genes from Zhang et al. [1]. The dN/dS ratios were estimated by PAML [18] program for the orthologs. Based on the CDS alignment of either protein coding data set, we used the one-ratio branch model to estimate the overall dN/dS ratios for each avian orthologous group and each mammalian orthologous group. In addition, to investigate the evolutionary rates in three major avian clades (Palaeognathae, Galloanserae and Neoaves), we used the three-ratio branch model, which estimated one identical dN/dS ratio for each clade. More details about dN/dS analyses are presented in Zhang et al. [1].

DNA sequence conservation

The overall level of conservation at the single nucleotide level could be estimated by PhastCons [19] based on multiple sequence alignments (MSA). First, the four-fold degenerate sites were extracted from 48-avian MSA and were used to estimate a neutral phylogenetic model by phyloFit [20], which is considered as the non-conserved model in PhastCons; we then ran PhastCons to estimate the conserved model. The conservation scores were predicted based on non-conserved and conserved models. We also used this method to estimate the sequence conservation for the 18-way mammalian genome alignments from the University of California at Santa Cruz (UCSC). Additional details of genome conservation are presented in the comparative genomics paper [1].

List of scripts used in avian comparative genome project

We also deposit the key scripts used in the avian comparative genome project in GigaDB [2], which include: 1) scripts for cleaning raw reads and assembling the genome using SOAPdenovo; 2) scripts for RepeatMasker and RepeatModeler repeat annotation; 3) scripts for homology-based protein-coding gene annotation and combining the gene annotation evidences into final gene sets; 4) scripts for generating whole genome alignment of multiple genomes; 5) scripts for running PAML to estimate branch model dN/dS ratios; 6) scripts for calculating conservation scores based on whole genome alignments and predicting highly conserved elements; 7) scripts for quantifying gene synteny percentages in birds and mammals; 8) scripts for identifying large segmental deletions from list of orthologous genes; 9) scripts for detecting gene loss in 48 avian genomes. We provide readme files in the script directories describing the usage of the scripts.

Availability and requirements

Download page for scripts:

https://github.com/gigascience/paper-zhang2014

Operating system: Linux

Programming language: Perl, R, Python

Other requirements: Some pipelines need external bioinformatics software, for which we provided executable files in the directories.

License: GNU General Public License version 3.0 (GPLv3)

Any restrictions to use by non-academics: No

Availability of supporting data

The NCBI BioProject/SRA/Study IDs for are listed in Additional file 2. Other data files presented in this data note are available in the GigaScience repository, GigaDB [2].

Authors’ information

The full author list of Avian Genome Consortium is provided in Additional file 1.

Additional file 1: Author list of the Avian Genome Consortium and contribution information of each author. (XLS 85 KB)

Additional file 2: NCBI accession numbers and GigaDB DOI for each bird. (XLS 46 KB)