1. Phrap assemblies visualized with the Consed (53) program.
Phrap assemblies visualized with the Consed (53) program. The consensus sequence is shown at the top of the display and is derived from aligned reads shown below the consensus. Note that the Phrap assembler uses the highest-quality base for the consensus regardless of base frequency at each position. Read identifiers and orientation (arrowheads) are shown on the left of the display. Low-quality bases and masked regions are grayed out. Green bars indicate sequence fragments found elsewhere in the assembly. (A) Example of a good-quality assembly with high read depth. Note the consistent alignment of all residues. (B) Example of a misassembled contig drawn together by a common repeat sequence (indicated by purple bars at left). Note the misaligned residues in red and the meaningless “consensus” sequence that does not correspond to any single read below it. (C) Chimeric contig produced by coassembly of closely related strains (haplotypes) in a metagenomic data set. Note that the consensus sequence is a chimera of the two haplotypes (based on the highest-quality base at each position) and likely does not represent an extant organism. (Screen shots are printed with permission of the software publisher.)‏
Victor Kunin et al. Microbiol. Mol. Biol. Rev. 2008; doi: /MMBR