![](images/graphics/blank.gif)
Sequence filtering
-
Accurate identification of real somatic variants is a primary part of cancer genome studies and precision oncology. However, artifacts introduced in various steps of sequencing obfuscate confidence in variant calling. Current computational approaches to variant filtering involve intensive interrogation of Binary Alignment Map (BAM) files and require massive computing power, data storage, and manual labor.
17p
vibransone
28-03-2024
2
2
Download
-
The identification of functional non-coding mutations is a key challenge in the field of genomics. Here we introduce μ-cisTarget to filter, annotate and prioritize cis-regulatory mutations based on their putative effect on the underlying “personal” gene regulatory network.
13p
vioraclene
31-03-2024
4
2
Download
-
In this study we generated a whole exome sequencing benchmark dataset using the platinum genome sample NA12878 and developed an intersect-then-combine (ITC) approach to increase the accuracy in calling single nucleotide variants (SNVs) and indels in tumour-normal pairs. We evaluated the effect of alignment, base quality recalibration, mutation caller and filtering on sensitivity and false positive rate.
11p
vioraclene
31-03-2024
4
2
Download
-
Here, we describe a novel approach for rapid discovery of a set of tumor-specific genomic structural variants (SVs), based on a combination of low coverage cancer genome sequencing using Oxford Nanopore with an SV calling and filtering pipeline. We applied the method to tumor samples of high-grade ovarian and prostate cancer patients and validated on average ten somatic SVs per patient with breakpoint-spanning PCR mini-amplicons.
14p
vibransone
28-03-2024
4
2
Download
-
Ebook "Kalman filtering and neural networks" includes content: Kalman filters, parameter based kalman filter training - theory and implementation, learning shape and motion from image sequences, chaotic dynamics, dual extended kalman filter methods, learning nonlinear dynamical system using the expectation maximization algorithm,.... and other contents.
298p
haojiubujain07
20-09-2023
10
3
Download
-
Part 1 of ebook "Python cookbook (Third edition)" provides readers with contents including: chapter 1 - data structures and algorithms; chapter 2 - strings and text; chapter 3 - numbers, dates, and times; chapter 4 - iterators and generators; chapter 5 - files and I/O; chapter 6 - data encoding and processing; chapter 7 - functions; chapter 8 - classes and objects;...
346p
hanlinhchi
29-08-2023
14
6
Download
-
The automated reconstruction of genome sequences in ancient genome analysis is a multifaceted process. Results: Here we introduce EAGER, a time-efficient pipeline, which greatly simplifies the analysis of large-scale genomic data sets. EAGER provides features to preprocess, map, authenticate, and assess the quality of ancient DNA samples. Additionally, EAGER comprises tools to genotype samples to discover, filter, and analyze variants.
14p
viaristotle
29-01-2022
7
0
Download
-
GetOrganelle is a state-of-the-art toolkit to accurately assemble organelle genomes from whole genome sequencing data. It recruits organelle-associated reads using a modified “baiting and iterative mapping” approach, conducts de novo assembly, filters and disentangles the assembly graph, and produces all possible configurations of circular organelle genomes.
31p
viarchimedes
26-01-2022
5
0
Download
-
The Cornales is the basal lineage of the asterids, the largest angiosperm clade. Phylogenetic relationships within the order were previously not fully resolved. Fifteen plastid genomes representing 14 species, ten genera and seven families of Cornales were newly sequenced for comparative analyses of genome features, evolution, and phylogenomics based on different partitioning schemes and filtering strategies.
14p
vilarryellison
29-10-2021
5
0
Download
-
De novo mutations (DNMs) are associated with neurodevelopmental and congenital diseases, and their detection can contribute to understanding disease pathogenicity. However, accurate detection is challenging because of their small number relative to the genome-wide false positives in next generation sequencing (NGS) data. Software such as DeNovoGear and TrioDeNovo have been developed to detect DNMs, but at good sensitivity they still produce many false positive calls.
7p
vibeauty
23-10-2021
8
1
Download
-
A seed location filter comes into play before alignment, discarding seed locations that alignment would deem a poor match. The ideal seed location filter would discard all poor match locations prior to alignment such that there is no wasted computation on unnecessary alignments.
18p
vibeauty
23-10-2021
9
1
Download
-
Database search has been the main approach for proteoform identification by top-down tandem mass spectrometry. However, when the target proteoform that produced the spectrum contains post-translational modifications (PTMs) and/or mutations, it is quite time consuming to align a query spectrum against all protein sequences without any PTMs and mutations in a large database.
13p
vitzuyu2711
29-09-2021
17
2
Download
-
Next-Generation Sequencing (NGS) has been widely accepted as an essential tool in molecular biology. Reduced costs and automated analysis pipelines make the use of NGS data feasible even for small labs, yet the methods for interpreting the data are not sophisticated enough to account for the amount of information.
12p
vigiselle2711
30-08-2021
11
1
Download
-
The ability to accurately and comprehensively identify genomic variations is critical for plant studies utilizing high-throughput sequencing. Most bioinformatics tools for processing next-generation sequencing data were originally developed and tested in human studies, raising questions as to their efficacy for plant research.
15p
visilicon2711
20-08-2021
7
1
Download
-
Microorganisms are not only indispensable to ecosystem functioning, they are also keystones for emerging technologies. Investigation of metabarcoding data should be done with care. Correct biological interpretation depends on several factors, including in-depth sequencing of the samples, choice of the most appropriate filtering strategy for the specific research goal, and use of family level for data clustering.
17p
vijeeni2711
30-06-2021
17
1
Download
-
Characterising genetic diversity through the analysis of massively parallel sequencing (MPS) data offers enormous potential to significantly improve our understanding of the genetic basis for observed phenotypes, including predisposition to and progression of complex human disease.
9p
viwyoming2711
16-12-2020
17
0
Download
-
High-throughput sequencing technologies are improving in quality, capacity and costs, providing versatile applications in DNA and RNA research. For small genomes or fraction of larger genomes, DNA samples can be mixed and loaded together on the same sequencing track.
10p
viwyoming2711
16-12-2020
11
0
Download
-
The production of multiple transcript isoforms from one gene is a major source of transcriptome complexity. RNA-Seq experiments, in which transcripts are converted to cDNA and sequenced, allow the resolution and quantification of alternative transcript isoforms.
18p
viwyoming2711
16-12-2020
12
1
Download
-
Let S be a standard r-graded ring and M be a finitely generated r-graded S -module. In this paper, we prove the existence of filter-regular sequences of M and then use them to study mixed multiplicities of M.
6p
tamynhan5
10-12-2020
11
3
Download
-
This paper proposes a method of artifact reduction in compressed videos using dynamic texture map together with artifact maps and 3D - fuzzy filters. To preserve better details during filtering process, the authors introduce a novel method to construct a texture map for video sequences called dynamic texture map. Then, temporal arifacts such as flicker artifacts and mosquito artifacts are also estimated by advanced flicker maps and mosquito maps. These maps combined with fuzzy filters are applied to intraframe and interframe pixels to enhance compressed videos.
10p
trinhthamhodang9
10-12-2020
8
0
Download
CHỦ ĐỀ BẠN MUỐN TÌM
![](images/graphics/blank.gif)