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De Novo Sequencing by SOLiD™ Next-Generation Sequencing
Superior coverage to get more genomes sequenced, and sequenced faster
The accuracy and throughput of the 5500xl Genetic Analyzer enables unparalleled de novo assembly of novel genomes, opening the way to detailed genetic analysis of any organism.
- Accuracy—ultra-deep sequencing capability combined with industry-leading, highly accurate 2-base color coding, plus Exact Call Chemistry (ECC), enables short-read assembly with less coverage
- Flexible file output—output files in base space or color space enable you to use the short-read assembler of your choice
- Throughput—generate over 20 Gb of sequence per day and get the coverage you need for high-confidence assembly
- Flexible library format—long-insert 2 x 60 mate pairs with your choice of insert size from 1 kb–6 kb, paired end reads, fragment reads, or a combination of library approaches, the flexible format FlowCells allow you to run them all simultaneously
- Coverage—long-insert mate pairs, ultra–high-throughput and industry-leading accuracy give you superior coverage to get more genomes sequenced, faster
Step-by-Step Guide to de novo Sequencing
When designing your own experiment, consider important parameters such as coverage, size, accuracy, and sensitivity; library type (fragment or mate paired?); and read length. Technical Considerations:
Learn More:
|
Learn More:
The SOLiD Community User documentation for the 5500 Series Genetic Analysis Systems can be found on the SOLiD Community. Access is through the 5500 Series User Hub. Access is limited to 5500 Series Genetic Analysis Systems users who are registered on the solid community and have been authenticated through the process of requesting permission to join the 5500 Series User Hub. |
Learn More: User documentation for the 5500 Series Genetic Analysis Systems can be found on the SOLiD Community. Access is through the 5500 Series User Hub. Access is limited to 5500 Series Genetic Analysis Systems users who are registered on the solid community and have been authenticated through the process of requesting permission to join the 5500 Series User Hub. 5500 Series User Hub |
The tools you need for each step in the de novo sequencingdata analysis workflow:
| Data Analysis Step | Applied Biosystems Software | 3rd-Party Software |
|---|---|---|
| 1. Align reads to reference in color space | ||
| 2. Generate quality metrics and perform mate pair rescue | ||
| 3. Generate sequencing and alignment statistics | ||
| 4. Identify Polymorphisms | ||
| 5. Translate color space to base space | ||
| 6. Visualize in context of annotation | ||
| 7. Convert SRF for publishing | ||
| *** Need XSQ --> csfasta/qual converter | ||
Learn more
The tools you need for each step in the de novo sequencing data analysis workflow:
Capillary electrophoresis-based de novo sequencing
When designing your own experiment, consider important parameters such as coverage, size, accuracy, and sensitivity; library type (fragment or mate paired?); and read length. Technical Considerations:
Learn More:
|
Learn More:
The SOLiD Community User documentation for the 5500 Series Genetic Analysis Systems can be found on the SOLiD Community. Access is through the 5500 Series User Hub. Access is limited to 5500 Series Genetic Analysis Systems users who are registered on the solid community and have been authenticated through the process of requesting permission to join the 5500 Series User Hub. |
Learn More: User documentation for the 5500 Series Genetic Analysis Systems can be found on the SOLiD Community. Access is through the 5500 Series User Hub. Access is limited to 5500 Series Genetic Analysis Systems users who are registered on the solid community and have been authenticated through the process of requesting permission to join the 5500 Series User Hub. 5500 Series User Hub |
The tools you need for each step in the de novo sequencingdata analysis workflow:
| Data Analysis Step | Applied Biosystems Software | 3rd-Party Software |
|---|---|---|
| 1. Align reads to reference in color space | ||
| 2. Generate quality metrics and perform mate pair rescue | ||
| 3. Generate sequencing and alignment statistics | ||
| 4. Identify Polymorphisms | ||
| 5. Translate color space to base space | ||
| 6. Visualize in context of annotation | ||
| 7. Convert SRF for publishing | ||
| *** Need XSQ --> csfasta/qual converter | ||
Learn more
The tools you need for each step in the de novo sequencing data analysis workflow:
Capillary electrophoresis-based de novo sequencing
Publications
- Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene lossPublication: BMC Genomics (2010)
- Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitismPublication: Science (2010)
- Complete genome sequence of corynebacterium pseudotuberculosis I19, a strain isolated from a cow in Israel with bovine mastitisPublication: J. Bacteriology (2010)
- First complete genome sequence of infectious laryngotracheitis virusPublication: JBMC Genomics (2011)
- Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study Publication: Journal of Microbiological Methods (2011)
Step-by-Step Guide to de novo Sequencing
When designing your own experiment, consider important parameters such as coverage, size, accuracy, and sensitivity; library type (fragment or mate paired?); and read length. Technical Considerations:
Learn More:
|
Learn More:
The SOLiD Community User documentation for the 5500 Series Genetic Analysis Systems can be found on the SOLiD Community. Access is through the 5500 Series User Hub. Access is limited to 5500 Series Genetic Analysis Systems users who are registered on the solid community and have been authenticated through the process of requesting permission to join the 5500 Series User Hub. |
Learn More: User documentation for the 5500 Series Genetic Analysis Systems can be found on the SOLiD Community. Access is through the 5500 Series User Hub. Access is limited to 5500 Series Genetic Analysis Systems users who are registered on the solid community and have been authenticated through the process of requesting permission to join the 5500 Series User Hub. 5500 Series User Hub |
The tools you need for each step in the de novo sequencingdata analysis workflow:
| Data Analysis Step | Applied Biosystems Software | 3rd-Party Software |
|---|---|---|
| 1. Align reads to reference in color space | ||
| 2. Generate quality metrics and perform mate pair rescue | ||
| 3. Generate sequencing and alignment statistics | ||
| 4. Identify Polymorphisms | ||
| 5. Translate color space to base space | ||
| 6. Visualize in context of annotation | ||
| 7. Convert SRF for publishing | ||
| *** Need XSQ --> csfasta/qual converter | ||
Learn more
The tools you need for each step in the de novo sequencing data analysis workflow:
Capillary electrophoresis-based de novo sequencing
When designing your own experiment, consider important parameters such as coverage, size, accuracy, and sensitivity; library type (fragment or mate paired?); and read length. Technical Considerations:
Learn More:
|
Learn More:
The SOLiD Community User documentation for the 5500 Series Genetic Analysis Systems can be found on the SOLiD Community. Access is through the 5500 Series User Hub. Access is limited to 5500 Series Genetic Analysis Systems users who are registered on the solid community and have been authenticated through the process of requesting permission to join the 5500 Series User Hub. |
Learn More: User documentation for the 5500 Series Genetic Analysis Systems can be found on the SOLiD Community. Access is through the 5500 Series User Hub. Access is limited to 5500 Series Genetic Analysis Systems users who are registered on the solid community and have been authenticated through the process of requesting permission to join the 5500 Series User Hub. 5500 Series User Hub |
The tools you need for each step in the de novo sequencingdata analysis workflow:
| Data Analysis Step | Applied Biosystems Software | 3rd-Party Software |
|---|---|---|
| 1. Align reads to reference in color space | ||
| 2. Generate quality metrics and perform mate pair rescue | ||
| 3. Generate sequencing and alignment statistics | ||
| 4. Identify Polymorphisms | ||
| 5. Translate color space to base space | ||
| 6. Visualize in context of annotation | ||
| 7. Convert SRF for publishing | ||
| *** Need XSQ --> csfasta/qual converter | ||
Learn more
The tools you need for each step in the de novo sequencing data analysis workflow:
Capillary electrophoresis-based de novo sequencing
Publications
- Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene lossPublication: BMC Genomics (2010)
- Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitismPublication: Science (2010)
- Complete genome sequence of corynebacterium pseudotuberculosis I19, a strain isolated from a cow in Israel with bovine mastitisPublication: J. Bacteriology (2010)
- First complete genome sequence of infectious laryngotracheitis virusPublication: JBMC Genomics (2011)
- Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study Publication: Journal of Microbiological Methods (2011)
For Research Use Only. Not for use in diagnostic procedures.