De novo transcriptome assembly with ABySS

By Inanç Birol, Shaun D. Jackman, C. Nielsen, Jenny Q. Qian, R. Varhol, Greg Stazyk, Ryan D. Morin, Yongjun Zhao, M. Hirst, Jacqueline E. Schein and 5 more. Bioinform., 2009

430 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/84d85eb47ecdbf5fa97003b8bc823c25ce08efa8

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Citations in the corpus

Cloud-scale RNA-sequencing differential expression analysis with Myrna (2010, background): “This categorization might be conducted comparatively with respect to a reference [4], by de novo assembly [5], or a combination of both [6-8].”
Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels (2012, positive): “For these cases, de novo genome assemblers have been employed to create transcript assemblies, or transfrags, from the RNA-seq reads in the absence of a reference genome (Birol et al., 2009; Collins et al., 2008; Jackson et al., 2009; Wakaguri et al, 2009). However, these short read genomic assemble”
Applications of next generation sequencing in molecular ecology of non-model organisms (2011, background): “However, since then, complete de novo assembly of Illumina/Solexa data has also been accomplished (Birol et al., 2009).”
Computational methods for transcriptome annotation and quantification using RNA-seq (2011, methodology): “use the reads to directly build consensus transcript”
Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data (2011, positive): “(1) ‘Mapping first’ approaches5, such as Scripture3 or Cufflinks2, first align all the reads to a reference (unannotated) genome and then merge sequences with overlapping alignment, spanning splice junctions with reads and paired-ends.”
Sequence assembly demystified (2013, background): “The curve corresponding to the ABySS2 assembly highlights an interesting artefact: this assembly contains more DNA than the other two but also greatly exceeds the actual size of the genome being assembled (as shown by the dashed line).”
Phylogeny of the manta and devilrays (Chondrichthyes: mobulidae), with an updated taxonomic arrangement for the family (2018, methodology): “6 (Birol et al., 2009) using multiple k-mer values (k = 51 to k = 251, in increments of 10).”
Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study (2011, methodology): “SOAPdenovo [8], ABySS [9], and Velvet-Oases (hereafter referred as Oases) [10] were reported to be successfully applied to transcriptome assembly of various organisms [3,9,11-13].”