HYbrid Assemblies: inconsistent read pairs

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chauser
Posts: 47
Joined: Wed Jan 31, 2007 3:34 pm

HYbrid Assemblies: inconsistent read pairs

Post by chauser » Tue Feb 11, 2014 11:56 pm

GEPers

In the hybrid assemblies, it would seem that the inconsistent read pairs warning (red triangles) "to far apart size compared to lib max" would not apply as there is no library?

Or, are these warnings to be ignored, or are they reflecting the size of the illumina reads?

Chuck

wleung
Posts: 185
Joined: Sun Feb 04, 2007 7:41 pm
Location: Washington University in St. Louis

Re: HYbrid Assemblies: inconsistent read pairs

Post by wleung » Wed Feb 12, 2014 2:10 am

While the "inconsistent read pairs" warning is correct, resolving misassemblies is beyond the scope of the current D. biarmipes sequence improvement project.

The Illumina reads for the D. biarmipes are paired end reads with a total length of 250bp. A subset (9 out of 19) 454 GS FLX Titanium runs for D. biarmipes contains mate pair reads with a total length of 2750bp.
D_biarmipes_paired_library_info.png
D_biarmipes_paired_library_info.png (190.06 KiB) Viewed 3010 times
Consed uses the placement of all the mate pair reads in an assembly to identify inconsistent mate pairs that are placed too close or too far apart. You can view this information by selecting "Info" -> "Library Info" in the Consed Main Window. Below is a sample screenshot from the project DBIA2377002 which shows the 454 paired reads have an average insert size of 2743bp and a standard deviation of 1241bp.
Dbiarmipes_library_info.png
Dbiarmipes_library_info.png (45.33 KiB) Viewed 3010 times
However, because of the limitation of the 454 platform, only a small fraction of the reads are paired. In addition, the Illumina paired end reads are not long enough to use them to be useful in resolving repetitive regions. Our initial assessment of the D. biarmipes assemblies suggests that there is insufficient number of paired 454 reads to resolve highly repetitive regions. Hence resolving misassemblies is not a primary goal of the D. biarmipes sequence improvement project.

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