Resources

LoReC – Coverage

LoReC – Coverage is a part of LoReC (Long-Read-Checker) toolkit.

LoReC – Coverage tool enables to analyse coverage depths of structural variants (SVs) or regions/genes of interest from long-read-sequencing (LRS) datasets obtained by all available technologies as well as short-read sequencing (SRS) datasets and optical genome mapping (OGM). The tool generates coverage statistics (min, max, Q1, Q3, mean, median) and/or coverage plots based on either the Binary Alignment Map (BAM) file(s) or OGM mapping files (CMAP, XMAP).

This tool is available as a platform-independent CLI application and is part of the Long-Read-Checker (LoReC) toolkit.

LoReC – Comparator

LoReC – Comparator is a part of LoReC (Long-Read-Checker) toolkit.

LoReC – Comparator tool enables to compare structural variants (SVs) from long-read-sequencing (LRS) datasets obtained by all available technologies as well as short-read sequencing (SRS) datasets and optical genome mapping (OGM). The tool enables to analyse targeted or whole-genome sequencing datasets using reference genome of interest. The SVs are compared based on defined parameters such as distance variance, intersection variance and size differences between individual SVs from the different technologies or variant callers. It offers several filtering options for particular SVs in base technology/dataset, including the closest SV in compared dataset(s), overlapping genes, variant types, and distance variance, intersection variance and size differences between datasets etc. Additionally, the tool provides possibility to annotate SVs using various databases such as the dbVar_Common, ClinVar or custom annotation file(s).

This tool is available as a platform-independent CLI application and is part of the LoReC toolkit.

Optimized hybrid data structure
based on the ternary search trees

The ZIP archive contains highly optimized hybrid data structure based on the ternary search trees and hash tables which can be used for indexing of genome data in form of k-mers obtained from genome in FASTA format. It also contains file parsers, utilities, suffix tree implementation, and test functions used for performance measurement. Source code is an attachment to Fast Hybrid Data Structure for a Large Alphabet K-Mers Indexing for Whole Genome Alignment article.

om-annotsv-svc:
Optical Mapping and AnnotSV Structural Variant Comparator

A software tool for comparison of structural variants identified by optical mapping technology (Bionano Genomics) and long-read next-generation sequencing technologies i.e. 10xGenomics, Oxford Nanopore Technologies and Pacific Biosciences. Structural variants produced by long-read next-generation sequencing technologies are analyzed using AnnotSV software tool. The tool computes the distance variance between the Bionano and AnnotSV genomic coordinates for the beginning and end of individual SVs. Various types of filtering, such as overlapping gene filter, variant type filter or distance sum variance filter can be used. The tool is provided as CLI application and is platform independent.

CLL calculator:
Application for Risk Assessment of Patients with Chronic Lymphocytic Leukemia

This software tool is used to calculate statistically significant rules over the data collection. It is assumed that the input file will contain the binary values of the attributes (DNA snips) of individual patients obtained during the examination. The outcome is represented by an evaluation of the chances of occurrence of the disease / complication. The tool supports the deciding making process whether to start or change the course of treatment.

OLGEN Coverage Limit calculator

The software allows to calculate the required coverage depth of the sequenced DNA segment to detect somatic mutations in the human genome. The software implements a newly designed probability model that calculates the required sequence coverage depth for a given n-percent somatic mutation and a defined error rate of measurement.

Periprosthetic Joint Infection Calculator

The software is created for clinicians' needs as a support tool for deciding on the patient's condition based on the laboratory results. The tool can be used in the fields of medicine and bioinformatics with a focus on clinical testing.

Total Knee Arthroplasty Revision Occurrence Calculator

The software is created for clinicians' needs to decide on the patient's condition and future TKA postoperative development based on clinical parameters and preoperative patient behavior. The tool can be used in the fields of medicine and bioinformatics with a focus on clinical testing.