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Description
This set of tracks displays four sub-scores generated by the assembly likelihood validator ALE (see references):
- Depth, measuring the evenness of sequencing depth (accounting for GC bias)
- Insert, quantifying how well the insert sizes of mapped reads matches the distribution expected from the sequencing library
- Placement, describing how well reads agree with the assembly given their probabilistic placement by the aligner.
- k-mer, the assembly distribution of k base pairs (default k=4bp), which serves as the Bayesian prior likelihood of assembly accuracy.
Display Conventions and Configuration
Each of the four subscore tracks is presented in WIG format. Each base is assigned a score in the ALE scoring framework, making WIG the ideal display format. The default display format is "full", designed to display one data point for each base. Displying in "dense" format may provide a more global perspective of the visualized region.
Methods
Raw reads were aligned to the assembly with SMALT version 0.7.0.1 (the aligner recommended for the REAPR assembly validator also used in this study), generating alignments in bam format. These alignments were used as inputs for ALE version 20130717, which gave as output the four statistically defined scores for each base in the assembly.
Credits
Please feel free to contact Owen Thompson with any questions and/or concerns regarding this or other tracks.
Thanks to the ALE team at the Joint Genome Institute and Cornell University for their contribution to assembly annotation. Thanks also to Hannes Ponstingl for his alignment algorithm SMALT.
References
Clark SC, Egan R, Frazier PI, Wang Z. ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies. Bioinformatics. 2013;29(4):435-43. PMID 23303509. Website.
Ponstingl, Hannes. (2012, May 11). SMALT - Sequence Mapping and Alignment Tool. Retrieved from http://www.sanger.ac.uk/resources/software/smalt.
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