[PDF] Top 20 A Crowdsourced Gameplay for Whole-Genome Assembly via Short Reads
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A Crowdsourced Gameplay for Whole-Genome Assembly via Short Reads
... sequence reads. After the selection, the player is di- rected to the gameplay interface shown in ...DNA reads to be aligned and merged that form a single ...DNA reads shown as puzzle blocks ... See full document
17
Separating metagenomic short reads into genomes via clustering
... separating short NGS reads from different ...on short reads, they explore the taxo- nomic content of metagenomic data according to known genomes rather than classifying ...classifies ... See full document
15
40124932fd563a4f53e59a813f8eb1aecc3febfc.pdf
... brought genome sequencing to the fingertips of groups and even individual ...the short reads into a finished genome represents a signifi- cant challenge, demanding highly specialized expertise ... See full document
12
Chromosomal-level assembly of the Asian seabass genome using long sequence reads and multi-layered scaffolding
... of genome expansion ...seabass genome (S6 ...most genome assemblies. The long sequencing reads spanned repeat-rich regions, providing an opportunity to resolve and characterize many tandem ... See full document
35
SyRI: finding genomic rearrangements and local sequence differences from whole genome assemblies
... long reads (sniffles and picky) or short reads (LUMPY) as input ...sequencing reads data as input, we simulated reads from the simulated genome and aligned them to the reference ... See full document
13
De novo assembly of the complex genome of Nippostrongylus brasiliensis using MinION long reads
... for short-read-based ...raw reads that were included in the output of the two methods (MinKNOW and Canu ...of reads exceeding the indicated ... See full document
18
Regulation of Yeast-to-Hyphae Transition in Yarrowia lipolytica
... the genome represented by the end of scaffold 14 in the parent strain genome assembly ...for short tandem repeats confirmed that the 5=-TTAGTCA GGG-3= repeats are common and identified ... See full document
18
Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads
... Measure, Rsem-Eval, and TransRate on identifying chimeric transcripts. In order to have our ground truth, we first identified which assembled transcripts are chi- meric with respect to a reference genome by using ... See full document
19
Nanopore sequencing and assembly of a human genome with ultra long reads
... our assembly we mapped previously generated whole- genome Illumina data (SRA:ERP001229) to each contig using BWA-MEM and corrected errors using ...our assembly to ...ambiguous ... See full document
65
Old can be new again: HAPPY whole genome sequencing, mapping and assembly
... Between 1995 and 2005, two general strategies were developed for sequencing a complete genome: the BAC by BAC sequencing [17] and shotgun se- quencing methods [18]. In the former approach, ge- nomic DNA is cut ... See full document
6
Application of Next-Generation Sequencing in Plant Breeding
... is genome editing, which is targeted gene modification to obtain a generation of new allelic variants in the ge- nomes of cultivated ...of genome sequences for many important crops, because of using NGS ... See full document
8
Superinfection exclusion and the long term survival of honey bees in Varroa infested colonies
... the genome whereas the Swindon DWV type A-B recombinant junction found here occurs in the structural region of the open reading frame (Figures 4 and ...full genome coverage was not achieved in both honey ... See full document
11
ScanIndel: a hybrid framework for indel detection via gapped alignment, split reads and de novo assembly
... supporting reads will often contain too few bases that match the reference and therefore fail to map; or the supporting reads may have one end map well to the reference genome but the rest of the ... See full document
12
Ribosome Profiling of Synechocystis Reveals Altered Ribosome Allocation at Carbon Starvation
... At the LC condition, the PS at start and stop codons increased (Fig. 4A and D), indicating that translation initiation and termination are slowed. The PS ramping in the 5= ends of ORFs was diminished at LC, suggesting a ... See full document
12
A high performance computational environment for UHTS studies
... concurrent execution feature to these components. This method allows to run these serial software with a good efficiency. Better performances can be archived using tools developed to run in a HPC system natively. A ... See full document
114
Analysis of the Aspergillus nidulans transcriptome using high-throughput RNA sequencing
... causing short interfering RNAs (siRNA) to mediate post-transcriptional gene silencing (PTGS), maintain genome integrity and protect against viruses (Taft et ... See full document
264
Simple sequence repeat variation in the Daphnia pulex genome
... pulex genome provides us with a valuable data set to study the mode and tempo of SSR evolution, without the inherent biases that accompany marker ...pulex genome with repeated motif sizes of 1-100 ... See full document
12
INSaFLU: an automated open web-based bioinformatics suite “from-reads” for influenza whole-genome-sequencing-based surveillance
... bioinformatics free web-based suite that deals with primary NGS data (reads) towards the automatic generation of the output data that are actually the core first-line “ genetic requests ” for effective and timely ... See full document
13
Analysis of gene expressions in both melanoma and melanocyte cell lines by chip-seq technology
... human genome in 2001, led by the revolutionary efforts of a number of research groups ...human genome and how it relates to the development of human malignant transformation genes of melanoma in this ... See full document
8
A cost effective and universal strategy for complete prokaryotic genomic sequencing proposed by computer simulation
... end reads, 90% of the 100 genome assemblies are less than 10 scaffolds and 95% of 100 genomes assemblies are less than 150 contigs (400 bp read ...the genome) of long repeats (> 300 bp), most of ... See full document
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