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A scaffold analysis tool using mate-pair information in genome sequencing.

Kim PG, Cho HG, Park K - J. Biomed. Biotechnol. (2008)

Bottom Line: Using end read pairs of fixed-sized mate-pair libraries, ConPath determines relative orientations of all contigs, estimates the gap size of each adjacent contig pair, and reports wrong assembly information by validating orientations and gap sizes.We have utilized ConPath in more than 10 microbial genome projects, including Mannheimia succiniciproducens and Vibro vulnificus, where we verified contig assembly and identified several erroneous contigs using the four types of error defined in ConPath.Also, ConPath supports some convenient features and viewers that permit investigation of each contig in detail; these include contig viewer, scaffold viewer, edge information list, mate-pair list, and the printing of complex scaffold structures.

View Article: PubMed Central - PubMed

Affiliation: SmallSoft Co., Ltd., Jang-Dong 59-5, Yusung-Gu, Daejeon 305-343, South Korea.

ABSTRACT
We have developed a Windows-based program, ConPath, as a scaffold analyzer. ConPath constructs scaffolds by ordering and orienting separate sequence contigs by exploiting the mate-pair information between contig-pairs. Our algorithm builds directed graphs from link information and traverses them to find the longest acyclic graphs. Using end read pairs of fixed-sized mate-pair libraries, ConPath determines relative orientations of all contigs, estimates the gap size of each adjacent contig pair, and reports wrong assembly information by validating orientations and gap sizes. We have utilized ConPath in more than 10 microbial genome projects, including Mannheimia succiniciproducens and Vibro vulnificus, where we verified contig assembly and identified several erroneous contigs using the four types of error defined in ConPath. Also, ConPath supports some convenient features and viewers that permit investigation of each contig in detail; these include contig viewer, scaffold viewer, edge information list, mate-pair list, and the printing of complex scaffold structures.

Show MeSH
Determining the relative orientations of contigs using mate-pair information. (a): b1 and g1 reads determine the relative orientation of contigs C1 and C2; (b): b2 and g2 reads determine the relative orientations of contigs C2 and C3; and (c): the relative orientations of contigs C1, C2, and C3 are determined by rotating the scaffold in Figure 2(b).
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fig3: Determining the relative orientations of contigs using mate-pair information. (a): b1 and g1 reads determine the relative orientation of contigs C1 and C2; (b): b2 and g2 reads determine the relative orientations of contigs C2 and C3; and (c): the relative orientations of contigs C1, C2, and C3 are determined by rotating the scaffold in Figure 2(b).

Mentions: Figure 2 shows the determination of the order and orientations of three contigs using two mate-pairs. In Figure 2(a), b1 and g1 readsdetermine the relative orientation of contigs C1 and C2,and, in the same way, b2 and g2 readsdetermine the relative orientations of contigs C2 and C3 (see Figure 2(b)). The relative orientations of contigs C1, C2, and C3 are determined by rotating the scaffold in Figure 2(b), as shown in Figure 2(c).


A scaffold analysis tool using mate-pair information in genome sequencing.

Kim PG, Cho HG, Park K - J. Biomed. Biotechnol. (2008)

Determining the relative orientations of contigs using mate-pair information. (a): b1 and g1 reads determine the relative orientation of contigs C1 and C2; (b): b2 and g2 reads determine the relative orientations of contigs C2 and C3; and (c): the relative orientations of contigs C1, C2, and C3 are determined by rotating the scaffold in Figure 2(b).
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2291285&req=5

fig3: Determining the relative orientations of contigs using mate-pair information. (a): b1 and g1 reads determine the relative orientation of contigs C1 and C2; (b): b2 and g2 reads determine the relative orientations of contigs C2 and C3; and (c): the relative orientations of contigs C1, C2, and C3 are determined by rotating the scaffold in Figure 2(b).
Mentions: Figure 2 shows the determination of the order and orientations of three contigs using two mate-pairs. In Figure 2(a), b1 and g1 readsdetermine the relative orientation of contigs C1 and C2,and, in the same way, b2 and g2 readsdetermine the relative orientations of contigs C2 and C3 (see Figure 2(b)). The relative orientations of contigs C1, C2, and C3 are determined by rotating the scaffold in Figure 2(b), as shown in Figure 2(c).

Bottom Line: Using end read pairs of fixed-sized mate-pair libraries, ConPath determines relative orientations of all contigs, estimates the gap size of each adjacent contig pair, and reports wrong assembly information by validating orientations and gap sizes.We have utilized ConPath in more than 10 microbial genome projects, including Mannheimia succiniciproducens and Vibro vulnificus, where we verified contig assembly and identified several erroneous contigs using the four types of error defined in ConPath.Also, ConPath supports some convenient features and viewers that permit investigation of each contig in detail; these include contig viewer, scaffold viewer, edge information list, mate-pair list, and the printing of complex scaffold structures.

View Article: PubMed Central - PubMed

Affiliation: SmallSoft Co., Ltd., Jang-Dong 59-5, Yusung-Gu, Daejeon 305-343, South Korea.

ABSTRACT
We have developed a Windows-based program, ConPath, as a scaffold analyzer. ConPath constructs scaffolds by ordering and orienting separate sequence contigs by exploiting the mate-pair information between contig-pairs. Our algorithm builds directed graphs from link information and traverses them to find the longest acyclic graphs. Using end read pairs of fixed-sized mate-pair libraries, ConPath determines relative orientations of all contigs, estimates the gap size of each adjacent contig pair, and reports wrong assembly information by validating orientations and gap sizes. We have utilized ConPath in more than 10 microbial genome projects, including Mannheimia succiniciproducens and Vibro vulnificus, where we verified contig assembly and identified several erroneous contigs using the four types of error defined in ConPath. Also, ConPath supports some convenient features and viewers that permit investigation of each contig in detail; these include contig viewer, scaffold viewer, edge information list, mate-pair list, and the printing of complex scaffold structures.

Show MeSH