Description

This track displays flags generated by the assembly validation algorithm REAPR (see references).

Display Conventions and Configuration

This track is presented in bed format. Each annotated region is present as a separate entry, and annotations may (and often do) overlap. The default display format is "squish" to facilitate compact visualization; expanding to "pack" or "full" will label each annotation according to its type.

Methods

Raw reads were aligned to the assembly with SMALT version 0.7.0.1 (the aligner recommended for the REAPR pipeline), generating alignments in bam format. These alignments were used as input for the "perfectmap" and "pipeline" algorithms within REAPR version 1.0.16, with an insert size equal to the mode of the insert sizes from the bam alignments.

Credits

Please feel free to contact Owen Thompson with any questions and/or concerns regarding this or other tracks.

Thanks to the REAPR team in Dr. Berriman's lab at the Wellcome Trust Sanger Institute for their contribution to assembly annotation. Thanks also to Hannes Ponstingl for his alignment algorithm SMALT.

References

Hunt M, Kikuchi T, Sanders M, Newbold C, Berriman M, Otto TD. REAPR: a universal tool for genome assembly evaluation. Genome Biol. 2013;14(5):R47. PMID 23710727

Ponstingl, Hannes. (2012, May 11). SMALT - Sequence Mapping and Alignment Tool. Retrieved from http://www.sanger.ac.uk/resources/software/smalt.