Description
This track displays alignments of de novo contigs (generated with the assembly program JR-Assembler and split by the assembly validation program REAPR) to the CB4856 reference genome with the Smith-Waterman Algorithm of BWA (BWA-SW).
Display Conventions and Configuration
Contig alignments are presented in bam 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). In regions of interest it may be useful to display read names, particularly where the assembly still fails to completely integrate complete contigs.
Methods
Contigs were generated with the Princeton dataset using JR-Assembler version 1.0.2 (including third-party utilities SSPACE 2.0, mdust, FLASH 1.2.7, and SOAPec 2.01). This process generated 12155 contigs, which were then split into 14167 contigs with REAPR version 1.0.16, a process requiring realignment of reads to contigs with the alignment program SMALT.
These contigs were then 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 data used to generate contigs displayed here is available from the Short Read Archive as experiment SRX1001806.
Thanks to the JR-Assembler team at the Institute of Information Science in Taipei, Taiwan, for their assistance running JR-Assembler.
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.
Thanks to Heng Li and Richard Durbin for their work developing BWA.
References
Chu TC, Lu CH, Liu T, Lee GC, Li WH, Shih AC. Assembler for de novo assembly of large genomes. Proc Natl Acad Sci USA. 2013;110(36):E3417-24. PMID 23966565. Website.
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. Website.
Ponstingl, Hannes. (2012, May 11). SMALT - Sequence Mapping and Alignment Tool. Retrieved from http://www.sanger.ac.uk/resources/software/smalt.
Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010;26(5):589-95. PMID 20080505.
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