Sequence assembly demystified

By Niranjan Nagarajan, Mihai Pop. Nature reviews genetics, 2013

463 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/a3a562ada6444727cc498ae8e966dec76036bcc1

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Citations in the corpus

Structural variant calling: the long and the short of it (2019, methodology): “We refer the interested reader to the review of Nagarajan and Pop [72], which provides a critical overview of de novo assembly methods.”
Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads (2016, background): “These repetitive sequences are approximately 5 kbp in length and have enough sequence similarity to each other to create fragmented shortread assemblies[45].”
A review of methods and databases for metagenomic classification and assembly (2019, methodology): “Genome assembly is a challenging problem, even for single genomes [98]; assembly of a mixed sample with many species in different abundances, as is necessary for a metagenomics sample, is even more complicated, requiring special-purpose assembly algorithms, reviewed and compared in [99, 100].”
The Genome 10K Project: A Way Forward (2015, unknown): “Armadillos (21, 1) Sloths (6, 1) Anteaters (4, 0)”
ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter (2016, unknown): “The problem refersto reconstructing the chromosome sequence(s) for a genome from sequencing reads, which are orders of magnitude shorter than the target genome (Nagarajan and Pop 2013).”
Integrating Hi-C links with assembly graphs for chromosome-scale assembly (2018, methodology): “Reads originating from the same locus are identified using assembly software, which can use these overlaps to reconstruct the genome sequence (Nagarajan and Pop, 2013; Miller et al., 2010).”
Oxford Nanopore MinION Sequencing and Genome Assembly (2016, background): “Nonetheless, PacBio reads have a significantly higher error rate ( 10% 15%) than SGS reads (<2%) [9].”
Assembling metagenomes, one community at a time (2017, background): “org/publicdomain/ze sequence data are fragmented, noisy, error prone and contain uneven sequencing depths [4].”
Microbial strain-level population structure and genetic diversity from metagenomes (2017, unknown): “Metagenomic assembly (Nagarajan and Pop 2013) provides one solution and has been successful in identifying strains of unchar-acterized species (Narasingarao et al. 2012; Brown et al. 2015).”
Assembling large genomes with single-molecule sequencing and locality-sensitive hashing (2014, background): “Genome assembly is the process of reconstructing a genome from a collection of short sequencing reads and is an integral step in any genome project 1,2 .”