Read alignment

Expansions of short tandem repeats are the cause of many neurogenetic disorders including familial amyotrophic lateral sclerosis, Huntington disease, and many others. Multiple methods have been recently developed that can identify repeat expansions in whole genome or exome sequencing data.

10p viellison 28-03-2024 3 1   Download

Powerful Vocabulary for Reading Success is the first vocabulary program to offer you a systematic, teacher-directed approach to improving your students’ reading achievement. This unique program is: Research-Based. Developed based on research that is proven effective for all students. Aligns to State Standards and No Child Left Behind for Vocabulary Development. Explicit and Comprehensive. An easy-to-manage, complete instructional program that models effective word learning and gives multiple exposures to hundreds of important words to ensure mastery.

121p haojiubujain05 09-08-2023 7 5   Download

Powerful Vocabulary for Reading Success is the first vocabulary program to offer you a systematic, teacher-directed approach to improving your students’ reading achievement. This book gives instruction for hundreds of high-utility, academic and content-area words and effective tools for deciphering hundreds more unknown words all found on state and national tests. A powerful combination for ensuring higher test scores. Powerful Vocabulary for Reading Success is the first vocabulary program to offer you a systematic, teacher-directed approach to improving your students’ reading achievement.

83p haojiubujain05 09-08-2023 9 5   Download

“15 minutes a day to hundreds of new words a year! Powerful Vocabulary for Reading Success is the first vocabulary program to offer you a systematic, teacher-directed approach to improving your students’ reading achievement. This unique program is: Research-Based Developed based on research that is proven effective for all students. Aligns to state standards and no child left behind for vocabulary development. Please refer to Ebook Powerful vocabulary for reading success: Grade 5 - Part 1 for more details.

124p haojiubujain05 09-08-2023 7 5   Download

Lecture Communication research: Asking questions, finding answers (4/e) - Chapter 13: Reading and writing the quantitative research report. After reading this chapter, you should be able to: Review and revise your literature review to ensure that the literature review aligns with the designed and tested study; review and revise, if necessary, the problem statement; review and revise, if necessary, the research questions and hypotheses presented in your study;...

11p haojiubujain04 27-07-2023 13 6   Download

In this paper we present IntroMap, a bioinformatics pipeline for the screening of candidate plants through the application of signal processing techniques to NGS data, using alignment to a reference genome sequence (annotation is not required) that shares homology with the recurrent parental cultivar, and without the need for de novo assembly of the read data or variant calling.

12p vinarcissa 21-03-2023 6 1   Download

The human genome contains “dark” gene regions that cannot be adequately assembled or aligned using standard short-read sequencing technologies, preventing researchers from identifying mutations within these gene regions that may be relevant to human disease.

23p vigalileogalilei 27-02-2022 9 1   Download

The vast quantities of short-read sequencing data being generated are often exchanged and stored as aligned reads. However, aligned data becomes outdated as new reference genomes and alignment methods become available.

6p vigalileogalilei 27-02-2022 9 1   Download

Tandemly repeated DNA is highly mutable and causes at least 31 diseases, but it is hard to detect pathogenic repeat expansions genome-wide. Here, we report robust detection of human repeat expansions from careful alignments of long but error-prone (PacBio and nanopore) reads to a reference genome.

17p vigalileogalilei 27-02-2022 9 1   Download

There is growing interest in using genetic variants to augment the reference genome into a graph genome, with alternative sequences, to improve read alignment accuracy and reduce allelic bias. While adding a variant has the positive effect of removing an undesirable alignment score penalty, it also increases both the ambiguity of the reference genome and the cost of storing and querying the genome index.

16p vigalileogalilei 27-02-2022 10 1   Download

We describe a method that adds long-read sequencing to a mix of technologies used to assemble a highly complex cattle rumen microbial community, and provide a comparison to short read-based methods. Long-read alignments and Hi-C linkage between contigs support the identification of 188 novel virus-host associations and the determination of phage life cycle states in the rumen microbial community.

18p vielonmusk 30-01-2022 15 0   Download

We present RaGOO, a reference-guided contig ordering and orienting tool that leverages the speed and sensitivity of Minimap2 to accurately achieve chromosome-scale assemblies in minutes. After the pseudomolecules are constructed, RaGOO identifies structural variants, including those spanning sequencing gaps.

17p vielonmusk 30-01-2022 5 0   Download

RNA sequencing using the latest single-molecule sequencing instruments produces reads that are thousands of nucleotides long. The ability to assemble these long reads can greatly improve the sensitivity of long-read analyses. Here we present StringTie2, a reference-guided transcriptome assembler that works with both short and long reads.

13p vielonmusk 30-01-2022 9 0   Download

Read alignment is the first step in most sequencing data analyses. Because a read’s point of origin can be ambiguous, aligners report a mapping quality, which is the probability that the reported alignment is incorrect. Despite its importance, there is no established and general method for calculating mapping quality.

12p vialfrednobel 29-01-2022 12 0   Download

Gene annotations, such as those in GENCODE, are derived primarily from alignments of spliced cDNA sequences and protein sequences. The impact of RNA-seq data on annotation has been confined to major projects like ENCODE and Illumina Body Map 2.0.

14p vialfrednobel 29-01-2022 10 0   Download

RNA-sequencing (RNA-seq) has a wide variety of applications, but no single analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data analysis, including experimental design, quality control, read alignment, quantification of gene and transcript levels, visualization, differential gene expression, alternative splicing, functional analysis, gene fusion detection and eQTL mapping.

19p viaristotle 29-01-2022 19 0   Download

Tandem repeat (TR) expansion is the underlying cause of over 40 neurological disorders. Long-read sequencing offers an exciting avenue over conventional technologies for detecting TR expansions. Here, we present Straglr, a robust software tool for both targeted genotyping and novel expansion detection from long-read alignments.

20p viarchimedes 26-01-2022 6 0   Download

Detecting multiplets in single nucleus (sn)ATAC-seq data is challenging due to data sparsity and limited dynamic range. AMULET (ATAC-seq MULtiplet Estimation Tool) enumerates regions with greater than two uniquely aligned reads across the genome to effectively detect multiplets. We evaluate the method by generating snATAC-seq data in the human blood and pancreatic islet samples.

19p viarchimedes 26-01-2022 8 0   Download

The accuracy of transcript quantification using RNA-seq data depends on many factors, such as the choice of alignment or mapping method and the quantification model being adopted. While the choice of quantification model has been shown to be important, considerably less attention has been given to comparing the effect of various read alignment approaches on quantification accuracy.

29p viarchimedes 26-01-2022 11 0   Download

Genome graphs can represent genetic variation and sequence uncertainty. Aligning sequences to genome graphs is key to many applications, including error correction, genome assembly, and genotyping of variants in a pangenome graph.

28p viarchimedes 26-01-2022 8 0   Download