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HipSTR / Haplotype inference and phasing for Short Tandem Repeats
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Allows genotyping, haplotyping, and phasing of short tandem repeats (STRs) from whole genome sequencing (WGS) data. HipSTR uses a multitude of inference techniques that integrate additional information about the haplotype in which the STR resides. The software enables specific detection of de novo STR variants. It is scalable and apt to the analysis of large-scale sequencing data and liable tool for genotyping STRs from Illumina sequencing data.
MISA-web / MIcroSAtellite identification tool
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Can retrieve sequences from the NCBI database by specifying the corresponding accession numbers in the input field. MISA-web is an extension to the command line tool MISA embedded into an easy-to-use web-based graphical user interface. MISA-web supports two different output formats: the proprietary MISA output format and generic GFF3. The GFF3 output format facilitates the integration of MISA-web search results in downstream analysis pipelines.
SSRIT / Simple Sequence Repeat Identification Tool
Finds all perfect simple sequence repeats (SSRs) in a given sequence. SSRIT provides a web app and a standalone version. This searching routine can be used to identify SSRs in different types of genomic DNA sequences, varying in size from several hundred nucleotides (BAC-end reads) up to 1 Mb of long contigs assembled from fully sequenced Bacterial Artificial Chromosome (BAC) and P1-derived Artificial Chromosome (PAC). It needs a sequence in FASTA format.
HySA / Hybrid Structural variant Assembly
Integrates sequencing reads from next-generation sequencing (NGS) and single-molecule sequencing (SMS) technologies to accurately assemble and detect structural variations (SV) in human genome. By identifying homologous SV-containing reads from different technologies through a bipartite-graph-based clustering algorithm, our approach turns a whole genome assembly problem into a set of independent SV assembly problems, each of which can be effectively solved to enhance assembly of structurally altered regions in human genome.
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An approach that uses a 'kmer' strategy to assemble misaligned sequence reads for predicting insertions, deletions, inversions, tandem duplications and translocations at base-pair resolution in targeted resequencing data. Variants are predicted by realigning an assembled consensus sequence created from sequence reads that were abnormally aligned to the reference genome. Using targeted resequencing data from tumor specimens with orthogonally validated SV, non-tumor samples and whole-genome sequencing data, BreaKmer had a 97.4% overall sensitivity for known events and predicted 17 positively validated, novel variants.
Is designed to search for microsatellite arrays, design primers, and tag primers using an automated routine. msatcommander accepts as input DNA sequence data in single-sequence or concatenated, FASTA-formatted files. msatcommander uses regular expression pattern matching within each DNA sequence to locate microsatellite arrays within user-selected repeat classes. Repeat sequences are located using their lowest alphabetical, noncomplementary designation, and repeat sequences fitting these designations are written to the summary output file. Search data and locus-specific primers are written to comma-separated value (CSV) files for subsequent use in spreadsheet or database programs. Binary versions of the graphical interface for msatcommander are available for Apple OS X and Windows XP. Users of other operating systems may run the graphical interface version using the available source code, provided their environment supports.
TSSV / Targeted characterisation of Short Structural Variation
A method for targeted profiling of short tandem repeats (STRs) that reports a full spectrum of all observed genomic variants along with their respective abundance. TSSV can accurately profile and characterize STRs without the use of a complete reference genome, and therefore minimizes biases introduced during the alignment and downstream analysis. TSSV scans sequencing data for reads that fully or partially encompass loci of interest based on the detection of unique flanking sequences. Subsequently, TSSV characterizes the sequence between a pair of non-repetitive flanking regions and reports statistics on known and novel alleles for each locus of interest.
SV2 / support-vector structural-variant genotyper
Implements a machine-learning algorithm for genotyping deletions and tandem duplications from paired-end whole genome sequencing (WGS) data. SV2 can rapidly integrate variant calls from multiple structural variant discovery algorithms into a unified callset with low rates of false discoveries and Mendelian errors, accurate de novo detection with no transmission bias in families. SV2 is an open source software written in Python that exploits read depth, discordant paired-ends, and split-reads in a supervised support vector machine classifier. Required inputs include a BAM file with supplementary alignment tags (SA), a Single-Nucleotide Variant (SNV) VCF file with allelic depth, and either a BED or VCF file of deletions and tandem duplications to be genotyped. The final product is a VCF file with genotypes and annotations for genes, repeats, and other befitting statistics for structural variant (SV) analysis.
An integrated structural variation (SV) caller which leverages multiple orthogonal SV signals for high accuracy and resolution. MetaSV proceeds by merging SVs from multiple tools for all types of SVs. It also analyzes soft-clipped reads from alignment to detect insertions accurately since existing tools underestimate insertion SVs. Local assembly in combination with dynamic programming is used to improve breakpoint resolution. Paired-end and coverage information is used to predict SV genotypes.
Alpha-CENTAURI / ALPHA satellite CENTromeric AUtomated Repeat Identification
Aims users to automate characterization of local centromeric tandem repeat sequence variation. alpha-CENTAURI is a bioinformatics pipeline for evaluating local higher-order repeat (HOR) structure across long read whole genome sequencing (WGS) datasets. With long-read data and a training dataset of repeat units from a satellite family of interest, this tool can predict patterns based on clustering discrete repeat units on each read.
smrt pipeline
Enables recovery of high identity allele structures for the sequence regions whose length was confirmed by Polymerase Chain Reaction (PCR) from cell line genomic DNA. smrt_pipeline is a method for the collection, processing and local assembly of single-molecule sequence data to form accurate contiguous local reconstructions. The pipeline incorporates Perl scripts for data download and downstream analysis. Also included in the pipeline are third-party assembly programs, managed by Perl wrapper scripts.
STRait Razor / Short Tandem Repeat allele identification tool Razor
A software tool to detect short tandem repeat (STR) alleles in massively parallel sequencing (MPS) raw data. The method of detection used by STRait Razor allows it to make reliable allele calls for all STR types in a manner that is similar to that of capillary electrophoresis. STRait Razor v2.0 incorporates several new features and improvements upon the original software, such as a larger default locus configuration file that increases the number of detectable loci (now including X-chromosome STRs and Amelogenin), an enhanced custom locus list generator, a novel output sorting method that highlights unique sequences for intra-repeat variation detection, and a genotyping tool that emulates traditional electropherogram data.
Facilitates regional overviews of Plasmodium vivax population genetic patterns in different endemic settings. vivaxGEN is an online platform that informs on the underlying transmission dynamics of this highly adaptive parasite. It also provides tools for standard population genetic analyses that can be applied to multiple sample batches to evaluate local and regional trends in the prevalence of polyclonal infections, population diversity, structure and differentiation both spatially and temporally.
SHEAR / Sample Heterogeneity Estimation and Assembly by Reference
A tool for next-generation sequencing data analysis that predicts SVs, accounts for heterogeneous variants by estimating their representative percentages, and generates personal genomic sequences to be used for downstream analysis. By utilizing structural variant detection algorithms, SHEAR also offers improved performance in the form of a stronger ability to handle difficult structural variant types and improved computational efficiency.
Proposes a dynamic programming based realignment method. STR-realigner considers repeat patterns in short tandem repeat (STR) regions as prior knowledge. By allowing the size change of repeat patterns with low penalty in STR regions, accurate realignment is expected. The effectiveness of the proposed realignment method for STR regions was verified from the comparison with an existing method on both simulation datasets and real whole genome sequencing dataset. STR-realigner shows the best performance in terms of consistency of the size of estimated STR regions in Mendelian inheritance.
Permits to automate and discover structural variations (SVs). Tardis is a toolkit that integrates read pair, read depth, and split read (using soft clipped mappings) sequence signatures to discover several types of SV, while resolving ambiguities among different putative SVs. This application is suitable for cloud use as the memory footprint is low. It is also capable of characterizing deletions, small novel insertions, tandem duplications, inversions, and mobile element retrotransposition.
TGS-TB / Total Genotyping Solution for Mycobacterium Tuberculosis
Facilitates multiple genotyping formats. TGS-TB is a web-based application that uses next-generation sequencing (NGS) for the analysis of phylogenies with (i) core genomic single nucleotide variations (SNVs), (ii) linkage network analysis of outbreak strains, (iii) spoligotyping, (iv) the analysis of IS6110 insertion sites and (v) variable number tandem repeat (VNTR). It also includes the prediction of Mycobacterium tuberculosis complex (MTBC) lineages/sub-lineages and potential antimicrobial resistance (AMR) based on the KvarQ script.
Allows users to model each variable number tandem repeats (VNTR), count repeat units, and detect sequence variation. adVNTR reports for any target VNTR in a donor an estimate of repeat unit (RU) counts and points mutations within the RUs. It trains Hidden Markov Models (HMMs) for each target VNTR locus, which provide the following advantages: (1) matching any portions of the unique flanking regions for read alignment; (2) separating homopolymer runs from other indels helping with frameshift detection; and (3) each VNTR can be modeled individually.
GtTR / Genotyping Tandem Repeats
Genotype tandem repeats (TRs) at population scale. GtTR is a probabilistic algorithm that genotypes TRs from short read sequencing data (targeted capture sequencing or whole genome sequencing) by comparison of regional read-depth with a single long-read reference sample. The algorithm can be used in combination with short read sequencing technologies to assess TR variation at a population scale. It was applied to Illumina targeted sequencing data to determine the genotypes of the targeted variable number tandem repeats (VNTR) regions.
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