Next Gen Sequencing 2008
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All leading sequencing technologies in one lab Genome sequencing using ABI 3730XL & SOLiD System Illumina Genome Analyzer & Roche GS FLX The next-gen sequencing technologies, embodied by the Roche GS FLX, the Illumina Genome Analyzer and the ABI SOLiD System, generate huge amounts of sequence information. The analysis and visualisation of these data is a crucial point in optimising data utility. ABI 3730XL
ABI SOLiD System
Roche GS FLX
Illumina Genome Analyzer
Read length
up to 1,100 bases/read
35 bp/read
Ø 250 bp/read
up to 50 bases/read
No. of reads
96 reads/run
85,000,000 (mate pair)
400,000 reads/run
40,000,000 reads/run
approx. 1 MB/day&system
3,000 MB/run/6days
100 MB/run/7.5 hours
2,000 MB/run/6.5 days
96 reactions/run
16 chambers (2 slides)
16 regions (1 plate)
8 channels (1 flowcell)
Raw data Samples/run
The reads of the 454 technology and Genome Analyzer/SOLiD with their high coverage can be optimally assembled with a low coverage of Sanger data to provide depth of sequence and a scaffold for assembly and finishing steps (hybrid strategy).
For de novo sequencing, a hybrid strategy of Sanger , 454 and short read sequencing with Genome Analyzer or SOLiD is highly recommended: - Sanger sequencing for repeats and gap closure - GS FLX sequencing for hard stops - Genome Analyzer sequencing for homopolymers
Data Assembly and Visualisation SeqMan Genome Assembler (SMGA) for Next Generation sequences assembles Illumina, 454 Life Sciences and Sanger data. Data files from SMGA can be imported into SeqMan Pro ™ to permit a wide range of sequence analyses and visualizations. SeqMan Pro™ can display electropherograms as well as flowgrams.
Data visualisation in GATC Genome Browser The GATC Genome Browser is an easy-to-use desktop application. It allows a convenient overview of e.g. whole genome de novo or re-sequencing, CHiP experiments or SAGE. The visualisation of the coverage helps to identify rearrangements within the genome, e.g. indels.
Indel GATC Biotech AG, Jakob-Stadler-Platz 7, 78467 Konstanz, Germany www.gatc-biotech.com In cooperation with DNASTAR Inc., 3801 Regent Street, Madison, WI 53705 USA www.dnastar.com
ABI SOLiD System
Roche GS FLX
Illumina Genome Analyzer
Read length
up to 1,100 bases/read
35 bp/read
Ø 250 bp/read
up to 50 bases/read
No. of reads
96 reads/run
85,000,000 (mate pair)
400,000 reads/run
40,000,000 reads/run
approx. 1 MB/day&system
3,000 MB/run/6days
100 MB/run/7.5 hours
2,000 MB/run/6.5 days
96 reactions/run
16 chambers (2 slides)
16 regions (1 plate)
8 channels (1 flowcell)
Raw data Samples/run
The reads of the 454 technology and Genome Analyzer/SOLiD with their high coverage can be optimally assembled with a low coverage of Sanger data to provide depth of sequence and a scaffold for assembly and finishing steps (hybrid strategy).
For de novo sequencing, a hybrid strategy of Sanger , 454 and short read sequencing with Genome Analyzer or SOLiD is highly recommended: - Sanger sequencing for repeats and gap closure - GS FLX sequencing for hard stops - Genome Analyzer sequencing for homopolymers
Data Assembly and Visualisation SeqMan Genome Assembler (SMGA) for Next Generation sequences assembles Illumina, 454 Life Sciences and Sanger data. Data files from SMGA can be imported into SeqMan Pro ™ to permit a wide range of sequence analyses and visualizations. SeqMan Pro™ can display electropherograms as well as flowgrams.
Data visualisation in GATC Genome Browser The GATC Genome Browser is an easy-to-use desktop application. It allows a convenient overview of e.g. whole genome de novo or re-sequencing, CHiP experiments or SAGE. The visualisation of the coverage helps to identify rearrangements within the genome, e.g. indels.
Indel GATC Biotech AG, Jakob-Stadler-Platz 7, 78467 Konstanz, Germany www.gatc-biotech.com In cooperation with DNASTAR Inc., 3801 Regent Street, Madison, WI 53705 USA www.dnastar.com
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