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Indel realignment software tools | High-throughput sequencing data analysis

Indel realignment software tools | High-throughput sequencing data analysis

Despite the fact that both Whole Exome Sequencing (WES) and Whole Genome Sequencing (WGS) have been widely used in biological studies and rare disease diagnosis, limitations of these techniques on insertion and deletion (INDEL calling are still not well characterized. INDELs, especially those disrupting protein-coding regions of the genome, have been strongly associated with human diseases. However, there are still many errors with INDEL variant calling, driven by library preparation, sequencing biases, and algorithm artifacts.
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GATK / Genome Analysis ToolKit
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Focuses on variant discovery and genotyping. GATK provides a toolkit, developed at the Broad Institute, composed of several tools and able to support projects of any size. The application compiles an assortment of command line allowing one to analyze of high-throughput sequencing (HTS) data in various formats such as SAM, BAM, CRAM or VCF. The website includes multiple documentation for guiding users.
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Octopus-toolkit
Examines epigenomic and transcriptomic next generation sequencing (NGS) data. Octopus-toolkit can be used for antibody- or enzyme-mediated experiments and studies for the quantification of gene expression. It can accelerate the data mining of public epigenomic and transcriptomic NGS data for basic biomedical research. This tool provides a private and a public mode: one to process the user’s own data, and the other to analyze public NGS data by retrieving raw files from the GEO database.
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ABRA / Assembly Based ReAligner
Allows next-generation sequencing read alignments. ABRA’s algorithm performs localized region assembly, contig building, alignment of assembled contigs and read realignment. The software identifies variations that are not present in the original read alignments and improves allele-frequency estimates for variations that are present. It can be used to enhance both germ-line and somatic variant detection and works with paired-end as well as single-end data.
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OMIndel
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Discovers large indels using optical maps (OM) reads with weak signal. OMIndel consists of an alignment-based method combined with local assembly-like approach. It records information of the discordance, including for instance the coordinates on the reference and sizing difference. This tool creates a graph for the discordant records and a graph-based union-find algorithm for retrieving all connected components of this graph.
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Genetic and metabolic regulation of Mycobacterium tuberculosis acid growth arrest
Tools (3): Trimmomatic, BWA, GATK
Topics (22): WES analysis, WGS analysis, RNA-seq analysis, sRNA-seq analysis, Mycobacterium tuberculosis, Infection, Gram-Positive Bacterial Infections, Ribonucleotides, Heterocyclic Compounds, 2-Ring, Purine Nucleotides, Carbon, Sugar Alcohols, Triose Sugar Alcohols, Pyridines, Isonicotinic Acids, Isoniazid, Hydroxy Acids, Heterocyclic Compounds, 4 or More Rings, Lactams, Macrocyclic, Amino Acids, Dicarboxylic, Excitatory Amino Acids, Amino Acids, Acidic
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