BOL: Related items

MUM&Co is a simple bash script that uses Whole Genome Alignment information provided by MUMmer (v4) to detect variants.

Rahul Nayak — Wed, 27 Apr 2022 04:34:12 -0500

MUM&Co is able to detect:
Deletions, insertions, tandem duplications and tandem contractions (>=50bp & <=150kb)
Inversions (>=1kb) and translocations (>=10kb)

Address of the bookmark: https://github.com/SAMtoBAM/MUMandCo

Genome Context Viewer (GCV)

LEGE — Sun, 21 May 2023 19:33:43 -0500

The Genome Context Viewer (GCV) is a web-app that visualizes genomic context data provided by third party services. Specifically, it uses functional annotations as a unit of search and comparison. By adopting a common set of annotations, data-store operators can deploy federated instances of GCV, allowing users to compare genomes from different providers in a single interface.

Address of the bookmark: https://github.com/legumeinfo/gcv

Tools to access the quality of your assembled genome !

LEGE — Thu, 08 Aug 2024 23:31:18 -0500

FASTA VALIDATOR + SEQKIT RMDUP: FASTA validation
GENOMETOOLS GT GFF3VALIDATOR: GFF3 validation
ASSEMBLATHON STATS: Assembly statistics
GENOMETOOLS GT STAT: Annotation statistics
NCBI FCS ADAPTOR: Adaptor contamination pass/fail
NCBI FCS GX: Foreign organism contamination pass/fail
BUSCO: Gene-space completeness estimation
TIDK: Telomere repeat identification
LAI: Continuity of repetitive sequences
KRAKEN2: Taxonomy classification
HIC CONTACT MAP: Alignment and visualisation of HiC data
MUMMER → CIRCOS + DOTPLOT & MINIMAP2 → PLOTSR: Synteny analysis
MERQURY: K-mer completeness, consensus quality and phasing assessment

Early Genome Screening: The New Health Horoscope!

LEGE — Thu, 02 Jan 2025 19:44:36 -0600

In an era where precision medicine is reshaping healthcare, genome screening is emerging as the modern equivalent of a health horoscope. It offers insights into our biological "stars," unraveling predispositions to various conditions and empowering individuals with knowledge to navigate their health journeys proactively. But how reliable is this "horoscope," and how does it impact our lives?

Understanding Genome Screening

Genome screening involves analyzing an individual's DNA to identify genetic variations that may influence health and disease susceptibility. This can range from simple single-gene tests to comprehensive whole-genome sequencing. By peering into our genetic blueprint, we can uncover risks for conditions like cancer, diabetes, cardiovascular diseases, and even rare genetic disorders.

The process is straightforward: a saliva or blood sample is collected, and advanced sequencing technologies decipher the genetic code. The results provide a personalized health map, guiding lifestyle modifications, preventive measures, or medical interventions.

A Shift from Reactive to Proactive Healthcare

Traditional healthcare often focuses on treating diseases after they manifest. Genome screening flips this model on its head, enabling a shift toward prevention and early intervention. For instance:

Cancer Risk Management: Individuals with BRCA1 or BRCA2 gene mutations can opt for enhanced screening programs or preventive surgeries to mitigate their risk of breast and ovarian cancers.
Cardiovascular Health: Genetic predispositions to conditions like familial hypercholesterolemia can prompt early cholesterol monitoring and lifestyle adjustments.
Rare Diseases: Identifying carriers of genetic disorders can aid in family planning and reduce the incidence of inherited conditions.

The Ethical and Practical Concerns

While genome screening offers incredible promise, it is not without challenges:

Accuracy and Interpretation: Genetic predisposition does not guarantee disease. Misinterpretation of results can lead to unnecessary anxiety or unwarranted medical interventions.
Privacy and Data Security: Genetic data is highly sensitive. Ensuring robust data protection measures is crucial to prevent misuse.
Accessibility and Equity: High costs and limited availability may restrict access to genome screening, exacerbating health disparities.

Balancing Science and Pseudoscience

The comparison of genome screening to horoscopes isn’t entirely unfounded. Both offer predictive insights, but the scientific foundation of genome screening distinguishes it from astrology. Unlike the alignment of celestial bodies, genetic predictions are based on rigorous data and evidence. However, the probabilistic nature of genetic predispositions underscores the importance of interpreting results in conjunction with clinical and lifestyle factors.

The Road Ahead

As genome screening becomes more affordable and integrated into routine healthcare, its potential to transform lives is immense. Policymakers, healthcare providers, and genetic counselors must collaborate to ensure ethical implementation, public awareness, and equitable access.

Imagine a future where your genetic "horoscope" is a trusted guide, not just a prediction. Early genome screening could help chart a healthier path for generations, making it a cornerstone of personalized medicine. After all, our genes might just hold the key to unlocking a future of better health and well-being.

HiTE: a fast and accurate dynamic boundary adjustment approach for full-length Transposable Elements detection and annotation in Genome Assemblies

LEGE — Sat, 20 Sep 2025 09:34:04 -0500

HiTE is a Python software that uses a dynamic boundary adjustment approach to detect and annotate full-length Transposable Elements in Genome Assemblies. In comparison to other tools, HiTE demonstrates superior performance in detecting a greater number of full-length TEs.

panHiTE

We have developed panHiTE, a comprehensive and accurate pipeline for TE detection in large-scale population genomes. It has been successfully applied to hundreds of plant population genomes, demonstrating its effectiveness and scalability.

For detailed instructions, please refer to the panHiTE tutorial.

Address of the bookmark: https://github.com/CSU-KangHu/HiTE

MOSS: A System for Detecting Software Similarity

Jit — Sat, 09 Dec 2017 08:59:07 -0600

Moss (for a Measure Of Software Similarity) is an automatic system for determining the similarity of programs. To date, the main application of Moss has been in detecting plagiarism in programming classes. Since its development in 1994, Moss has been very effective in this role. The algorithm behind moss is a significant improvement over other cheating detection algorithms (at least, over those known to us).

Moss can currently analyze code written in the following languages:

C, C++, Java, C#, Python, Visual Basic, Javascript, FORTRAN, ML, Haskell, Lisp, Scheme, Pascal, Modula2, Ada, Perl, TCL, Matlab, VHDL, Verilog, Spice, MIPS assembly, a8086 assembly, a8086 assembly, MIPS assembly, HCL2.

Address of the bookmark: https://theory.stanford.edu/~aiken/moss/

kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity

Rahul Nayak — Tue, 29 May 2018 08:37:53 -0500

The k-mer Weighted Inner Product.

This software implements a de novo, alignment free measure of sample genetic dissimilarity which operates upon raw sequencing reads. It is able to calculate the genetic dissimilarity between samples without any reference genome, and without assembling one.

De novo estimates of genetic relatedness from next-gen sequencing data https://kwip.readthedocs.org

Address of the bookmark: https://github.com/kdmurray91/kwip

TARDIS: Toolkit for automated and rapid discovery of structural variants

Neel — Fri, 09 Jun 2017 04:43:31 -0500

tardis

Toolkit for Automated and Rapid DIscovery of Structural variants

Requirements

zlib (http://www.zlib.net)
mrfast (https://github.com/BilkentCompGen/mrfast)
htslib (included as submodule; http://htslib.org/)
Fetching tardis

git clone https://github.com/BilkentCompGen/tardis.git --recursive

https://github.com/BilkentCompGen/tardis

Address of the bookmark: https://github.com/BilkentCompGen/tardis

ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information

BioJoker — Sun, 20 Jan 2019 06:34:36 -0600

ClipCrop for detecting SVs with single-base resolution using soft-clipping information. A soft-clipped sequence is an unmatched fragment in a partially mapped read. To assess the performance of ClipCrop with other SV-detecting tools, we generated various patterns of simulation data – SV lengths, read lengths, and the depth of coverage of short reads – with insertions, deletions, tandem duplications, inversions and single nucleotide alterations in a human chromosome.

Address of the bookmark: https://github.com/shinout/clipcrop

vsFilt: A tool to improve virtual screening by structural filtration of docking poses

Neel — Wed, 25 Nov 2020 02:39:16 -0600

The vsFilt is the first open application for post-docking structural filtration, available as a web-server. The new tool is easy to use and configure to detect a wide range of interaction types that are known to be involved in molecular recognition, including hydrogen and halogen bonds, ionic interactions, hydrophobic contacts, π-stacking, and cation-π interactions. The web-server can process large libraries of up to 150’000 docked ligand poses. The results are web-based and can be operated on-line using the built-in HTML5 interactive analysis tools, or can be downloaded for a local use. The vsFilt is freely available on-line, no login required.

Address of the bookmark: https://biokinet.belozersky.msu.ru/vsfilt