Hawkeye Launch Pad

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The Launch Pad is the first window displayed in Hawkeye and acts as an overview and portal to your assembly. Its tabbed interface displays high level statistics, feature, library, scaffold, contig, and read information. The Launch Pad is interactive, so that you can select a feature, scaffold, contig, or read, and the display will focus on that object. At the very top is a Menu Bar, followed by a row of controls. The Contig ID Spin Box allows you to jump to a particular contig, and see the currently active contig. The "All Views" button displays both the Scaffold and Contig views while the "Scaffold View" and "Contig View" buttons display just that view respectively. Below that is a tabbed display showing different aspects of your assembly, as explained below.


Statistics

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Launch Pad Statistics Tab

The initial display shows high level statistics. The left side table has common assembly size statistics explained such as average and N50 scaffold and contig sizes. An explaination of these metrics is provided here. To the right of this table is a graphical display of the scaffolds (top) and contigs (bottom). The size of the rectangles indicates the size of objects. The color of the rectangle indicates the number of features found in that scaffold or contig (red=high count, green=low count). You can mouse over any rectangle to view its id, size, and feature count, or double click on a rectangle to open separate Scaffold and Contig displays. The barchart can also be sorted by feature count, so that contigs will be ranked by their likelihood of misassembly, or as a spacefiling treemap to better utilize the space available. Below we can see visually there are 3 large scaffolds which account for most of the bases in the assembly.



Features

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Launch Pad Features Tab

The next tab is labeled "Features" and displays a table of the features in your assembly. AMOS comes bundled with tools for creating several types of features for mis-assembly detection, such as high occurence of compressed or expanded mates, regions of correlated SNPs, or read alignment breakpoint positions. The feature tab allows you to see which contigs have a high number of features, and a report on what type of features are present. Double Clicking on a feature displays that region in the scaffold and contig windows if they are open. If they are not open, click the "All views", "Scaffold View", or "Contig View" to display that region. A radio button groups features by the contig they occur in, or the type of feature. Click on the column headers to sort by that column.



Libraries

The next tab is labeled "Libraries" and displays a table of the inserts and libraries in your assembly. The Mean and Standard Deviations columns reflect the sizes specified by the input files, the Inserts column is the number of inserts in the entire bank. Select an insert by clicking on its row. Then Click one of the Distribution buttons at the bottom to see a histogram of those values. "Insert Size" is the histogram of inserts sizes for inserts in contigs in the assembly; "Read Clear Range" is the histogram of clear range length for all reads in the library (not necessarily in a contig); "Read Length" is the full length of all reads in that library; and "GC Content" is the GC Content of all reads in that library.

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Launch Pad Libraries Tab
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Insert Size Histogram



Scaffolds

The next tab is labeled "Scaffolds" and displays a table of scaffolds in your assembly. Click on the column headers to sort by that column. Click the plus box to see which contigs are in that scaffold. Double clicking on any scaffold or contig displays it in the scaffold and contig windows if they are open. If not, click one of the view buttons to display that scaffold or contig. At the bottom of the table are search boxes to search for a scaffold or contig by name, and buttons to display the span of scaffolds as a barchart as on the Statistics view, or a histogram of contigs per scaffold.

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Launch Pad Scaffold Tab
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Scaffold Span Chart


Contigs

The next tab is labeled "Contigs" and displays a table of contigs in your assembly. Click on the column headers to sort by that column. At the bottom are search boxes to search for a particular contig by name. Next to that is a click box to also display read information for each contig. Note this can take a long time and use a lot of memory if your assembly has many reads (more than 100k reads). If the Display Reads checkbox is displayed, then you can expand the plus next to each contig to see which reads are present in each contig. Double click on a contig or read to display it in the scaffold or contig views if they are open, or double click and click on a View button at the top to display it. In the bottom right are buttons to display an barchart of the contig sizes, a histogram of reads per contig, and a plot of GC content of your reads.

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Launch Pad Contig Tab
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Contig Size Chart as a treemap


Reads

The next tab is labeled "Reads" and displays a table of reads in the current contig. Click on the column headers to sort by the column. At the bottom are search boxes to search for a particular read by name. Next to the search boxes are buttons to display a histograms of read length and GC content of the reads in the current contig. Double click on a read to jump to that read in the scaffold or contig view.

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Launch Pad Read Tab
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Read Length Histogram