Visualizing a human genome

Here you can visually probe a DISCOVAR de novo assembly of a human genome. The DNA for this demo comes from the GM12878 immortalized cell line, from a woman of European ancestory who lived in Utah.

To see part of the assembly graph, enter a command in the box below. For example

H     will get you help and     S=11:90.26M D=1

will get you the part of the assembly aligning to the human reference sequence at position 90.26 megabases on chromosome 11, and extending into the graph to depth 1. This example exhibits a 31 kb sequence that is present on one copy of chr 11 in GM12878 but not present in the reference.

DISCOVAR de novo is work in progress that we'll gradually roll out. This demo is for revision 50090 of the code.

Understanding the graphs. Each edge represents one strand of a DNA sequence. The sequences themselves are here. Edges are color-coded by length: gray < black < red < magenta. Brown edges represent captured gaps. Edges are labeled by index, length (for longer edges), aligned position on the reference, and copy number where known (1.00x means predicted to represent the two homologous chromosomes at one locus). Red vertices denote points that 'continue on' in the full graph.


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