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2023•Cambridge University Press eBooksRequires access

Fragment assembly

Veli Mäkinen, Djamal Belazzougui, Fabio Cunial, Alexandru I. Tomescu

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Abstract

Throughout the book we mostly assume the genome sequence under study to be known. In this chapter we look at strategies for how to assemble fragments of DNA into longer contiguous blocks, and eventually into chromosomes. This chapter is partitioned into sections roughly following the workflow of a de novo assembly project, namely, error correction, contig assembly, scaffolding, and gap filling. Algorithms working with de Bruijn graphs and overlap graphs are studied.

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What this paper is about

Throughout the book we mostly assume the genome sequence under study to be known. In this chapter we look at strategies for how to assemble fragments of DNA into longer contiguous blocks, and eventually into chromosomes. This chapter is partitioned into sections roughly following the workflow of a de novo assembly project, namely, error correction, contig assembly, scaffolding, and gap filling. Algorithms working with de Bruijn graphs and overlap graphs are studied.

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Available abstract

Throughout the book we mostly assume the genome sequence under study to be known. In this chapter we look at strategies for how to assemble fragments of DNA into longer contiguous blocks, and eventually into chromosomes. This chapter is partitioned into sections roughly following the workflow of a de novo assembly project, namely, error correction, contig assembly, scaffolding, and gap filling. Algorithms working with de Bruijn graphs and overlap graphs are studied.

Key concepts: De Bruijn sequence, Contig, Sequence assembly, De Bruijn graph, Fragment (logic), Computer science, Workflow, Sequence (biology)

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