Description

This track displays alignments of CB4856 Sanger reads generated by the Moerman lab at the Universty of British Columbia and by Washington University in St. Louis.

Display Conventions and Configuration

Sanger bam alignments are presented in "squish" display format, without read names displayed, using a greyscale to display mapping quality. All alignments are shown by default (i.e. even those with mapping quality = 0) and paired end reads are joined.

Methods

Sanger reads were aligned to the CB4856 reference genome with BWA 0.7.2, using the "bwasw" utility with default settings.

Credits

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

The raw Sanger reads displayed here can be made available by the Moerman or Waterston Labs upon request; at this time we have not deposited these reads to the SRA because they were generated as part of separate experiments/investigations, and are used here in a post hoc analysis to provide validation to the CB4856 assembly. Note that reads from UBC begin with "WRMHS" and are paired, while reads from WU are named with regular expressions matching ^[a-z]+[0-9]+[a-z][0-9]+ and are not paired.

Thanks to Heng Li and Richard Durbin for their work developing BWA.

References

Perkins, J. D., 2010 Comparison of fosmid libraires made from two geographic isolates of Caenorhabditis elegans, University of British Columbia. Link.

Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010;26(5):589-95. PMID 20080505.