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MToolBox
An effective workflow with customizable parameters and able to analyze multiple samples in a single run. MToolBox is the only tool that generates as output a VCF file, the standard format for large-scale genotyping information, suitably customized for mitochondrial data, by including the heteroplasmy fraction and its related confidence interval. Additionally, MToolBox provides the user with essential analyses of reconstructed mitochondrial genomes, i.e. haplogroup assignment and variant prioritization, exploiting a broad collection of annotation resources. Thus, MToolBox may provide a valuable support for the recognition of candidate mitochondrial mutations in clinical studies.
mtDNA-Server
A web server based on Hadoop, allowing to analyze human mitochondrial next-generation sequencing (NGS) data. All aspects from sequence alignment of FASTQ raw data to final results including heteroplasmic variants are covered. By hiding all complex workflow steps, we provide the mitochondrial DNA (mtDNA) research community an easy to use web server, allowing the detection of heteroplasmic variants in a secure and reproducible way. The validation of the integrated heteroplasmy approach shows that mtDNA-Server detects heteroplasmic variants and sample contamination accurately. The within-sample contamination detection based on mitochondrial haplogroups has significant general potential to assess data from whole genome sequencing studies for potential contamination and is therefore not limited to target mtDNA sequencing. mtDNA-Server is conceived to handle large amount of mtDNA NGS data, by taking advantage of parallel data processing using the MapReduce framework, having the main focus on ease of use and reliability of the results to prevent erroneous conclusions.
mit-o-matic
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A tool designed to provide clinically relevant information distributed in disparate resources for understanding and annotating human mitochondrial DNA variations. The pipeline has two components: a command-line component that provides automation for alignment of NGS reads to the modified rCRS; and an online version that provides a comprehensive genetic report of mitochondrial variants, which includes information about the corresponding mutation, gene, associated phenotype and population frequency. mit-o-matic also reports the estimated haplogroup, disease associated variations and heteroplasmic sites.
fastMitoCalc
Estimates Mitochondrial DNA (mtDNA) copy number highly accurately using 0.1% of the genome. fastMitoCalc is an application that takes advantage of the indexing of sequencing alignment files, focusing on a small subset of the nuclear genome to estimate autosomal DNA coverage accurately. It analyzes hundreds of thousands of genomes currently being sequenced by large research consortia, and facilitates association studies of mtDNA copy number with quantitative trait values or nuclear variants.
Norgal / de Novo ORGAneLle extractor
Extracts mitochondrial DNA from whole genome sequencing (WGS) data. Norgal is an assembly method that allows extraction and assembly full or partial mitochondrial and chloroplast genomes from WGS short reads, especially in situations where reference sequences are unavailable. The mitochondrial genome of the Oriental hornet (Vespa orientalis) was published using a Norgal assembly. The software thus contributes to the field of discovering and assembling novel mitochondrial sequences from WGS data.
MitoSuite
Allows users to analyze data from high-throughput sequencing (HTS) of the human mitochondrial genome. MitoSuite is a graphical tool that supports quality check of alignment data, variant annotation, building consensus sequences, haplogroup classification, and detection of heteroplasmic sites, exogenous contamination, and base-substitution patterns for mitochondrial genome data obtained by HTS. The software is especially designed for non-bioinformaticians unfamiliar with typing complicated commands.
MitoBamAnnotator
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A simple web-based tool for analyzing heteroplasmy using sequences generated by second generation sequencing technology, specifically designed for studying the functional potential of mtDNA heteroplasmy in humans. MitoBamAnnotator receives files describing the alignment of mtDNA next generation sequences to the mtDNA genome or a list of mutated positions as input, and provides a richly annotated report of suspected heteroplasmic sites. Users control the filtration process by modifying the filtration parameters, and receive the results in a compact table which can be further filtered using spreadsheet editing programs such as Microsoft Excel or open-access equivalents.
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