JR-Contigs cm Track Settings
 
JR-Contig cross_match Alignments (Reapr Processed)   (All Alignments tracks)

Display mode:   

Display read names
Attempt to join paired end reads by name
Minimum alignment quality:

Alignment Gap/Insertion Display Options Help on display options
Draw double horizontal lines when both genome and query have an insertion
Draw a vertical purple line for an insertion at the beginning or end of the
query, orange for insertion in the middle of the query

Additional coloring modes:
Color by strand (blue for +, red for -)
Use gray for
Use R,G,B colors specified in user-defined tag
No additional coloring

Display data as a density graph:

BAM configuration help

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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 aligner cross_match.

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 cross_match, the alignments converted to bam format, and all indels were shifted to the left with custom scripts.

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 Phil Green at the University of Washington for his aligner cross_match.

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.