SOLiD bioinformatics workshop Part I
I almost missed this workshop because I was told by my colleague that it’s just another seminar on SOLiD. Luckily I emailed the sales rep and received the agenda the night before. I think Analisa Resources Sdn. Bhd did a great job organizing this workshop. Not to mention the wonderful buffet lunch at Hotel Equatorial. :p
Illumina Solexa and SOLiD are two NGS platforms that came up almost the same time. Despite similar read length, SOLiD can generate twice the amount of sequence at a slightly lower cost. Judging from the number of publications, it is assumed that most people favour Solexa over SOLiD. But, the scenario is changing.
SOLiD differs from other platforms in which the reads are mapped in colour space. Its 2-base encoding system allows better SNPs detection by differentiating a SNP from sequencing error. Two colour change will indicate a SNPs while single colour change indicates an error.
Despite what paper reviews said about SOLiD, here’s the things they can’t tell you
• Since Invitrogen has acquired Applied Biosystems (not the other way around) last year, Applied Biosystems now provide end-to-end solutions from sample preparation to sequencing.
• SOLiD can run two slides per run. Each slide can be divided up to 8 chambers. With its barcoding system, up to 320 samples can be run each time (with 20 barcodes).
• Both 454 and SOLiD uses emulsion PCR concept but the difference is SOLiD places the bead randomly on the flow cell (That’s how they claim the throughout is increased). But now, they are looking into ways to increase bead density by arranging beads on the slide.
• The new SOLiD version 3 allows users to view the sequencing process via the internet and control the process remotely.
• SOLiD will give forward and reverse reads (This is new to me. I wonder if other platforms can do the same)
• Besides higher accuracy 99.96%, SOLiD offers different size of insert size up to 4 kb to enable scaffolding. Scaffolding is important to form larger contigs.
• Unlike other sequencing platform, SOLiD user can download data analysis softwares from the website and sample data. http://www.solidsoftwaretools.com
Related posts:
SOLiD Bioinformatics Part II: de novo assembly
SOLiD Bioinformatics Part III: SOLiD softwares
Illumina Solexa and SOLiD are two NGS platforms that came up almost the same time. Despite similar read length, SOLiD can generate twice the amount of sequence at a slightly lower cost. Judging from the number of publications, it is assumed that most people favour Solexa over SOLiD. But, the scenario is changing.
SOLiD differs from other platforms in which the reads are mapped in colour space. Its 2-base encoding system allows better SNPs detection by differentiating a SNP from sequencing error. Two colour change will indicate a SNPs while single colour change indicates an error.
Despite what paper reviews said about SOLiD, here’s the things they can’t tell you
• Since Invitrogen has acquired Applied Biosystems (not the other way around) last year, Applied Biosystems now provide end-to-end solutions from sample preparation to sequencing.
• SOLiD can run two slides per run. Each slide can be divided up to 8 chambers. With its barcoding system, up to 320 samples can be run each time (with 20 barcodes).
• Both 454 and SOLiD uses emulsion PCR concept but the difference is SOLiD places the bead randomly on the flow cell (That’s how they claim the throughout is increased). But now, they are looking into ways to increase bead density by arranging beads on the slide.
• The new SOLiD version 3 allows users to view the sequencing process via the internet and control the process remotely.
• SOLiD will give forward and reverse reads (This is new to me. I wonder if other platforms can do the same)
• Besides higher accuracy 99.96%, SOLiD offers different size of insert size up to 4 kb to enable scaffolding. Scaffolding is important to form larger contigs.
• Unlike other sequencing platform, SOLiD user can download data analysis softwares from the website and sample data. http://www.solidsoftwaretools.com
Related posts:
SOLiD Bioinformatics Part II: de novo assembly
SOLiD Bioinformatics Part III: SOLiD softwares
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