Sequences alignment
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Ebook "Introduction to computational biology: An evolutionary approach" Analysis of molecular sequence data is the main subject of this introduction to computational biology. There are two closely connected aspects to biological sequences: (i) their relative position in the space of all other sequences, and (ii) their movement through this sequence space in evolutionary time. Accordingly, the first part of the book deals with classical methods of sequence analysis: pairwise alignment, exact string matching, multiple alignment, and hidden Markov models.
329p tracanhphuonghoa1007 22-04-2024 10 2 Download
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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
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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
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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
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Ebook "Developing bioinformatics computer skills" includes content: Audience for this book, biology in the computer age, computational approaches to biological questions, setting up your workstation, files and directories in unix, working on a unix system, biological research on the web, sequence analysis, pairwise alignment, and database searching,...and other contents.
344p haojiubujain07 20-09-2023 4 2 Download
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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
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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
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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
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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
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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
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The ability to inexpensively describe taxonomic diversity is critical in this era of rapid climate and biodiversity changes. The recent genome-skimming approach extends current barcoding practices beyond short markers by applying low-pass sequencing and recovering whole organelle genomes computationally.
20p vigalileogalilei 27-02-2022 14 1 Download
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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
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Alignment-free (AF) sequence comparison is attracting persistent interest driven by data-intensive applications. Hence, many AF procedures have been proposed in recent years, but a lack of a clearly defined benchmarking consensus hampers their performance assessment.
18p vielonmusk 30-01-2022 16 0 Download
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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
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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
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Alignment-free methods, more time and memory efficient than alignment-based methods, have been widely used for comparing genome sequences or raw sequencing samples without assembly.
17p vielonmusk 30-01-2022 10 0 Download
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Although Kraken’s k-mer-based approach provides a fast taxonomic classification of metagenomic sequence data, its large memory requirements can be limiting for some applications. Kraken 2 improves upon Kraken 1 by reducing memory usage by 85%, allowing greater amounts of reference genomic data to be used, while maintaining high accuracy and increasing speed fivefold.
13p vielonmusk 30-01-2022 9 0 Download
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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
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Genomic differences range from single nucleotide differences to complex structural variations. Current methods typically annotate sequence differences ranging from SNPs to large indels accurately but do not unravel the full complexity of structural rearrangements, including inversions, translocations, and duplications, where highly similar sequence changes in location, orientation, or copy number.
13p vielonmusk 30-01-2022 47 0 Download
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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