[PDF] Top 20 A new algorithm for de novo genome assembly
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A new algorithm for de novo genome assembly
... of de novo genome assembly. Some of the de novo genome assemblers ...a genome, while others (e.g., ABySS and SOAPdenovo) use a de Bruijn graph ...the ... See full document
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Error Correction and de novo Genome Assembly of DNA Sequencing Data
... a new algorithm and implementation of the overlap graph construction that works in parallel, and we have parallelized most of the pipeline in ...the assembly process in SAGE was very aggressive, ... See full document
143
De novo genome assembly of Geosmithia morbida, the causal agent of thousand cankers disease
... Many tree fungal pathogens associate with bark beetles in the family Scolytinae (Six & Wingfield, 2011). With climate change, beetles and their fungal symbionts can invade new territory and become major ... See full document
12
An Escherichia coli ST131 pangenome atlas reveals population structure and evolution across 4,071 isolates
... quality-control, genome de novo assembly, DNA read mapping and ESBL gene screening in the largest ST131 set examined thus far to reconstruct a core genome phylogeny and evaluated the ... See full document
13
Resequencing and assembly of seven complex loci to improve the Leishmania major (Friedlin strain) reference genome
... Friedlin genome sequence using an in house Python ...the new assembled genome using Bowtie2 [21] with default parameters in order to verify the consistency of the assem- bled ...Friedlin ... See full document
13
Bridger: a new framework for de novo transcriptome assembly using RNA seq data
... complete genome sequences from the same or related ...for de novo transcriptome assembly by introducing an auxiliary graph, without the help of any genomic in- ...all de novo ... See full document
10
De novo sequence assembly of Albugo candida reveals a small genome relative to other biotrophic oomycetes
... Whole genome shotgun sequencing was carried out for ...ome assembly was performed using version 2.3 of the Newbler assembly software (Roche/454 Brandford CT, ...Ac2VRR genome data has been ... See full document
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De novo assembly of the complex genome of Nippostrongylus brasiliensis using MinION long reads
... We sequenced DNA extracted from a population of adult N. brasiliensis resident in the small intestine of a rat using R9.4 flow cells on a MinION Mk1b. DNA preparation and sequencing was managed by ONT. Four sample ... See full document
18
MGERT: a pipeline to retrieve coding sequences of mobile genetic elements from genome assemblies
... or de novo ...[31–33]. De novo approaches - as it could be inferred from its name - requires no previous knowledge of repeat content of the ...or genome self-alignment ...popular ... See full document
8
Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples
... Our newly developed viral sequencing protocol combines selective depletion of contaminating carrier RNA and host rRNA with unbiased total RNA-seq of randomly-primed cDNA. It thereby improves the quality of raw sequencing ... See full document
12
Complete genome sequence of Thermus brockianus GE-1 reveals key enzymes of xylan/xylose metabolism
... final de novo assembly obtained three circular contigs, providing the complete genome sequence of ...and genome coverage of ...quiver algorithm, included in PacBio SMRT Analysis, ... See full document
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Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus)
... High molecular weight DNA was extracted from leuko- cytes collected from a female mouse lemur born and housed at the Duke Lemur Center (DLC Animal ID: 7030). DNA extraction followed the BNG human blood DNA isolation ... See full document
17
SQUID: transcriptomic structural variation detection from RNA seq
... first algorithm to detect TSVs accurately and comprehensively that targets both tradi- tional fusion-gene detection and the much broader class of general ...of de novo transcriptome assembly ... See full document
16
Combining de novo and reference-guided assembly with scaffold_builder
... reference genome and the hits are parsed with Show-coords ...The algorithm then proceeds along the reference sequence and inserts an appropriate number of Ns between every pair of non- overlapping ... See full document
5
Clustering of Short Read Sequences for de novo Transcriptome Assembly
... an algorithm to assemble transcriptome ...an algorithm for transcriptome assembly in the absence of a reference ...using de Bruijn graph with different k-mer ...proposed algorithm is ... See full document
10
Metassembler: merging and optimizing de novo genome assemblies
... CEGMA algorithm [9], as well as the concordance of the metassembly sequence with remapped paired-end and mate-pair reads using REAPR ...the assembly sequence as a proxy for the completeness and accuracy of ... See full document
10
Whole-Genome Sequencing of the Akata and Mutu Epstein-Barr Virus Strains
... De novo assembly of EBV ...deduplication algorithm. In preparation for EBV de novo assem- bly, the deduplicated sequencing data were precleared of non-EBV se- ...the ... See full document
11
Methods for De-novo Genome Assembly
... platforms, de-novo genome assembly remains a chal- lenging ...Nanopore), genome assembly has evolved to respond to the changes in input data ...for genome assembly; ... See full document
20
Superinfection exclusion and the long term survival of honey bees in Varroa infested colonies
... same colony on Big Island contained a nearly equal mix of type A and B (93 014X coverage), whereas Varroa from Oahu (314 713X coverage) was domi- nated by type A (Figure 3b). A switch in dominance between type A and B in ... See full document
11
De novo transcriptomic assembly and mRNA expression patterns of Botryosphaeria dothidea infection with mycoviruses chrysovirus 1 (BdCV1) and partitivirus 1 (BdPV1)
... Pear ring rot, caused by the destructive pathogen Botryosphaeria, is responsible for substantial eco- nomic losses through widespread fruit rots and stem canker. This caused a severe recession in the growth of pear fruit ... See full document
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