Name
Title | ||
|---|---|---|
Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data. |
Abstract | ||
|---|---|---|
White spruce (Picea glauca) is a dominant conifer of the boreal forests of North America, and providing genomics resources for this commercially valuable tree will help improve forest management and conservation efforts. Sequencing and assembling the large and highly repetitive spruce genome though pushes the boundaries of the current technology. Here, we describe a whole-genome shotgun sequencing strategy using two Illumina sequencing platforms and an assembly approach using the ABySS software. We report a 20.8 giga base pairs draft genome in 4.9 million scaffolds, with a scaffold N50 of 20,356 bp. We demonstrate how recent improvements in the sequencing technology, especially increasing read lengths and paired end reads from longer fragments have a major impact on the assembly contiguity. We also note that scalable bioinformatics tools are instrumental in providing rapid draft assemblies.The Picea glauca genome sequencing and assembly data are available through NCBI (Accession#: ALWZ0100000000 PID: PRJNA83435). http://www.ncbi.nlm.nih.gov/bioproject/83435. |
Year | DOI | Venue |
|---|---|---|
2013 | 10.1093/bioinformatics/btt178 | Bioinformatics |
Keywords | Field | DocType |
illumina sequencing platform,assembly approach,picea glauca genome sequencing,picea glauca,current technology,assembly contiguity,gb white,assembly data,giga base pairs draft,sequencing technology,whole-genome shotgun,rapid draft assembly,genomics | Genome,Shotgun sequencing,Giga-,Biology,Illumina dye sequencing,Genomics,DNA sequencing,Bioinformatics,Sequence assembly | Journal |
Volume | Issue | ISSN |
29 | 12 | 1367-4811 |
Citations | PageRank | References |
10 | 0.70 | 7 |
Authors | ||
24 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Inanc Birol | 1 | 78 | 9.34 |
| Anthony Raymond | 2 | 18 | 1.94 |
| Shaun D Jackman | 3 | 72 | 7.37 |
| Stephen Pleasance | 4 | 10 | 0.70 |
| Robin Coope | 5 | 10 | 1.04 |
| Greg A Taylor | 6 | 10 | 0.70 |
| Macaire Man Saint Yuen | 7 | 10 | 0.70 |
| Christopher I Keeling | 8 | 10 | 0.70 |
| Dana Brand | 9 | 10 | 0.70 |
| Benjamin Vandervalk | 10 | 121 | 9.60 |
| Heather Kirk | 11 | 10 | 0.70 |
| Pawan Pandoh | 12 | 10 | 0.70 |
| Richard A. Moore | 13 | 19 | 1.38 |
| Yongjun Zhao | 14 | 10 | 0.70 |
| Andrew J Mungall | 15 | 15 | 1.19 |
| Barry Jaquish | 16 | 10 | 0.70 |
| Alvin Yanchuk | 17 | 10 | 0.70 |
| Carol Ritland | 18 | 10 | 0.70 |
| Brian Boyle | 19 | 10 | 0.70 |
| Jean Bousquet | 20 | 10 | 0.70 |
| Kermit Ritland | 21 | 10 | 0.70 |
| John MacKay | 22 | 27 | 2.67 |
| Jörg Bohlmann | 23 | 10 | 1.04 |
| Steven J M Jones | 24 | 10 | 0.70 |