De Novo Assembly Samples Page
The Assembly workflow enables de novo assembly of a reference genome directly from the sequencing reads. Because assembly relies upon significant coverage of the reference genome, this workflow is best suited for the assembly of bacterial genomes (such as E. coli). The assembly process is performed by the Velvet software.
The Secondary Analysis Summary pane provides access to three graphs, described below.
Low Percentage refers to run statistics that should be near 0 for an ideal run.
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y-axis |
x-axis |
Description |
|---|---|---|
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Percent |
Mismatch 1 |
The average percentage of mismatches for Read 1 over all cycles. |
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Mismatch 2 |
The average percentage of mismatches for Read 2 over all cycles. |
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Phasing 1 |
The percentage of molecules that fall behind (fail to incorporate a base) in a sequencing cycle in Read 1. |
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Phasing 2 |
The percentage of molecules that fall behind (fail to incorporate a base) in a sequencing cycle in Read 2. |
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PrePhasing 1 |
The percentage of molecules that run ahead (incorporate an extra base) in a sequencing cycle in Read 1. |
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PrePhasing 2 |
The percentage of molecules that run ahead (incorporate an extra base) in a sequencing cycle in Read 2. |
High Percentage refers to run statistics that should all be close to 100% for a good run.
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y-axis |
x-axis |
Description |
|---|---|---|
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Percent |
|20/|1 1 |
The ratio of intensities at cycle 20 to the intensities at cycle 1 for Read 1. |
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|20/|1 2 |
The ratio of intensities at cycle 20 to the intensities at cycle 1 for Read 2. |
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Align 1 |
The percentage of clusters that aligned to the reference in Read 1. |
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Align 2 |
The percentage of clusters that aligned to the reference in Read 2. |
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PE Orientation |
The percentage of paired-end alignments with the expected orientation. |
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PE Resynthesis |
The ratio of first cycle intensities for Read 1 to first cycle intensities for Read 2. |
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PF |
The percentage of clusters passing filters. |
A cluster represents a clonal spot on the flow cell that contains the amplified DNA strands that will be sequenced.
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y-axis |
x-axis |
Description |
|---|---|---|
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Clusters |
Raw |
The total number of clusters detected in the run. |
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PF |
The total number of clusters passing filter in the run. |
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Unaligned |
The total number of clusters passing filter that did not align to the reference genome, if applicable. Clusters that are unindexed are not included in the unaligned count. |
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Unindexed |
The total number of clusters passing filter that were not associated with any index sequence in the run. |
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Duplicate |
The total number of clusters for a paired-end sequencing run which are considered to be PCR duplicates. |