PLoS ONE, 2020 The chloroplast genome harbors plenty of valuable information for phylogenetic research. Illumina short-read data is generally used for de novo assembly of whole plastomes.
Agnes Scheunert +3 more
doaj +1 more source
Identification of optimum sequencing depth especially for de novo genome assembly of small genomes using next generation sequencing data. [PDF]
PLoS ONE, 2013 Next Generation Sequencing (NGS) is a disruptive technology that has found widespread acceptance in the life sciences research community. The high throughput and low cost of sequencing has encouraged researchers to undertake ambitious genomic projects ...
Aarti Desai +7 more
doaj +1 more source
MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph [PDF]
, 2014 MEGAHIT is a NGS de novo assembler for assembling large and complex metagenomics data in a time- and cost-efficient manner. It finished assembling a soil metagenomics dataset with 252Gbps in 44.1 hours and 99.6 hours on a single computing node with and ...
Lam, Tak-Wah +4 more
core +2 more sources
Plant assemble - Plant de novo genome assembly: assembly v2
, 2022 With the advancement of long-read sequencing technologies and associated bioinformatics tools, it has now become possible to de novo assemble complex plant genomes with unrivalled contiguity, completeness and correctness. As read lengths can surpass repeat lengths, the ability to assemble genomes de novo has dramatically improved, whereby complex plant
Scott Ferguson +2 more
openaire +1 more source
Tedna: a transposable element de novo assembler [PDF]
Bioinformatics, 2014 Abstract Motivation : Recent technological advances are allowing many laboratories to sequence their research organisms. Available de novo assemblers leave repetitive portions of the genome poorly assembled. Some genomes contain high proportions of transposable elements, and transposable elements appear to be a major force behind ...
Zytnicki, Matthias +2 more
openaire +3 more sources
Pattern formation during de novo assembly of the Arabidopsis shoot meristem [PDF]
, 2007 Most multicellular organisms have a capacity to regenerate tissue after wounding. Few, however, have the ability to regenerate an entire new body from adult tissue. Induction of new shoot meristems from cultured root explants is a widely used, but poorly
Das, Pradeep +5 more
core +2 more sources
Metassembler: merging and optimizing de novo genome assemblies [PDF]
Genome Biology, 2015 AbstractGenome assembly projects typically run multiple algorithms in an attempt to find the single best assembly, although those assemblies often have complementary, if untapped, strengths and weaknesses. We present our metassembler algorithm that merges multiple assemblies of a genome into a single superior sequence.
Wences, A. H., Schatz, M. C.
openaire +3 more sources
Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies [PDF]
PeerJ, 2017 Background De novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality
Cédric Cabau +5 more
doaj +2 more sources
De Novo Assembly of Nucleotide Sequences in a Compressed Feature Space [PDF]
, 2017 Sequencing technologies allow for an in-depth analysis of biological species but the size of the generated datasets introduce a number of analytical challenges.
Robertson, David L., Tapinos, Avraam
core +1 more source
De novo assembly of transcriptomes from a B73 maize line introgressed with a QTL for resistance to gray leaf spot disease reveals a candidate allele of a lectin receptor-like kinase [PDF]
, 2020 Gray leaf spot (GLS) disease in maize, caused by the fungus Cercospora zeina, is a threat to maize production globally. Understanding the molecular basis for quantitative resistance to GLS is therefore important for food security.
Berger, Dave K. +6 more
core +2 more sources