Accurate alignment tools

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-Seq has become one of the most widely used applications based on next-generation sequencing technology. However, raw RNA-Seq data may have quality issues, which can significantly distort analytical results and lead to erroneous conclusions. Therefore, the raw data must be subjected to vigorous quality control (QC) procedures before downstream analysis. Currently, an accurate and complete QC of RNA-Seq data requires of a suite of different QC tools used consecutively, which is inefficient in terms of usability, running time, file usage, and interpretability of the results.

10p vibeauty 23-10-2021 11 0   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

Although software tools abound for the comparison, analysis, identification, and classification of genomic sequences, taxonomic classification remains challenging due to the magnitude of the datasets and the intrinsic problems associated with classification.

21p visilicon2711 20-08-2021 4 1   Download

The time required to analyse RNA-seq data varies considerably, due to discrete steps for computational assembly, quantification of gene expression and splicing analysis. Recent fast non-alignment tools such as Kallisto and Salmon overcome these problems, but these tools require a high quality, comprehensive reference transcripts dataset (RTD), which are rarely available in plants.

17p viansan2711 30-07-2021 27 1   Download

The development of next-generation sequencing instruments has led to the generation of millions of short sequences in a single run. The process of aligning these reads to a reference genome is time consuming and demands the development of fast and accurate alignment tools.

25p viwyoming2711 16-12-2020 10 1   Download

Metagenomics has a great potential to discover previously unattainable information about microbial communities. An important prerequisite for such discoveries is to accurately estimate the composition of microbial communities. Most of prevalent homology-based approaches utilize solely the results of an alignment tool such as BLAST, limiting their estimation accuracy to high ranks of the taxonomy tree.

13p vikentucky2711 26-11-2020 10 1   Download

Protein sequence alignment is essential for a variety of tasks such as homology modeling and active site prediction. Alignment errors remain the main cause of low-quality structure models. A bioinformatics tool to refine alignments is needed to make protein alignments more accurate.

7p vikentucky2711 24-11-2020 13 1   Download

Genome sequencing provides a powerful tool for pathogen detection and can help resolve outbreaks that pose public safety and health risks. Mapping of DNA reads to genomes plays a fundamental role in this approach, where accurate alignment and classification of sequencing data is crucial.

9p viflorida2711 30-10-2020 17 2   Download

In this paper, we introduce a multilingual access and retrieval system with enhanced query translation and multilingual document retrieval, by mining bilingual terminologies and aligned document directly from the set of comparable corpora which are to be searched upon by users. By extracting bilingual terminologies and aligning bilingual documents with similar content prior to the search process provide more accurate translated terms for the in-domain data and support multilingual retrieval even without the use of translation tool during retrieval time....

4p hongphan_1 15-04-2013 46 2   Download