Computational Comparison of Human Genomic Sequence Assemblies for a Region of Chromosome 4

Abstract

Much of the available human genomic sequence data exist in a fragmentary draft state following the completion of the initial high-volume sequencing performed by the International Human Genome Sequencing Consortium (IHGSC) and Celera Genomics (CG). We compared six draft genome assemblies over a region of chromosome 4p (D4S394-D4S403), two consecutive releases by the IHGSC at University of California, Santa Cruz (UCSC), two consecutive releases from the National Centre for Biotechnology Information (NCBI), the public release from CG, and a hybrid assembly we have produced using IHGSC and CG sequence data. This region presents particular problems for genomic sequence assembly algorithms as it contains a large tandem repeat and is sparsely covered by draft sequences. The six assemblies differed both in terms of their relative coverage of sequence data from the region and in their estimated rates of misassembly. The CG assembly method attained the lowest level of misassembly, whereas NCBI and UCSC assemblies had the highest levels of coverage. All assemblies examined included <60% of the publicly available sequence from the region. At least 6% of the sequence data within the CG assembly for the D4S394-D4S403 region was not present in publicly available sequence data. We also show that even in a problematic region, existing software tools can be used with high-quality mapping data to produce genomic sequence contigs with a low rate of rearrangements.[All sequence accessions for the genomic sequence assemblies analyzed and the data sets used to assess coverage and rates of misassembly are available from http://www.ed.ac.uk/∼csemple.]

A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome

“…A major misassembly occurs when two distinct regions of the genome are joined (usually in a repeat), creating an artificial translocation event [9-13]. Major misassemblies are relatively rare but they are known to occur in nearly all established WGS assemblers and are extremely difficult to detect without a finished sequence or physical map [28-31]. We identified 13 alignment conflicts that were indicative of a major misassembly, and that linked 22 bins into eight 'spiders', so-called because of the branching structure created by the misassembly (Figure 2).…”

Segments missing from the draft human genome sequence can be isolated by transformation‐associated recombination cloning in yeast

“…In this study, end‐sequence analysis of YAC/BACs with random DNA inserts revealed differences from the published genome sequence in a significant fraction of clones, indicating potential errors in the corresponding contigs. Similar discrepancies have also been described in other reports (Aach et al ., 2001; Katsanis et al ., 2001; Christian et al ., 2002; Semple et al ., 2002). TAR cloning could be a powerful tool for the verification of contig assembly, as we showed for two contigs on chromosome 5.…”

Single Nucleotide Polymorphisms Caused by Assembly Errors

“…These are mainly compression and expansion errors due to improper handling of repeats which, together with expensive gap closing, are left to fix in the finishing phase. 4–6 Currently and in the light of high speed data generation, most exciting is the size of data a modern assembler can handle. But what about the qualities of assembled genome contigs which have passed the usual first tests of validation?…”