BOL: Related items

GMOL: An Interactive Tool for 3D Genome Structure Visualization

Jit — Wed, 21 Mar 2018 12:25:20 -0500

GMOL was developed based upon our multi-scale approach that allows a user to scale between six separate levels within the genome. With GMOL, a user can choose any unit at any scale and scale it up or down to visualize its structure and retrieve corresponding genome sequences.

Address of the bookmark: https://www.nature.com/articles/srep20802

SynVisio: An Interactive Multiscale Synteny Visualization Tool for McScanX.

Jit — Sun, 31 May 2020 02:01:14 -0500

SynVisio lets you explore the results of McScanX a popular synteny and collinearity detection toolkit and generate publication ready images.

SynVisio requires two files to run:

The simplified gff file that was used as an input for a McScanX query.
The collinearity file generated as an output by McScanX for the same input query.
Optional track file in bedgraph format to annotate the generated charts.

SynVisio offers different types of visualizations such as Linear Parallel plots, Hive plots, Stacked Parallel Plots and Dot plots. Users can configure the type of plots required and then choose the source and the target chromosomes that need to be mapped. Users also have option to download the generated visualizations in publication ready SVG or PNG formats.

Address of the bookmark: https://synvisio.github.io/#/

Panacus : A Counting Tool for Pangenome Graphs

Neel — Fri, 14 Jun 2024 14:42:28 -0500

panacus is a tool for calculating statistics for GFA files. It supports GFA files with P and W lines, but requires that the graph is blunt, i.e., nodes do not overlap and consequently, each link (L) points from the end of one segment (S) to the start of another.

panacus supports the following calculations:

coverage histogram
pangenome growth statistics
path-/group-resolved coverage table

Address of the bookmark: https://github.com/marschall-lab/panacus

From DNA Chaos to a Clear Microbial Story

BioStar — Fri, 21 Aug 2026 11:22:54 -0500

Imagine opening a metagenomic dataset and finding millions of DNA fragments, each carrying a tiny piece of information about the microbial world inside a sample. The challenge is not generating the data — it is turning that data into a meaningful story.

This is where MeTAline comes in.

MeTAline is a reproducible workflow designed to simplify shotgun metagenomic analysis. It brings together important steps such as quality control, host-DNA removal, taxonomic profiling and functional analysis, using tools including Kraken2, MetaPhlAn4 and HUMAnN.

What makes it especially useful is its ability to handle large datasets while keeping analyses organized and reproducible. Built with Snakemake and supporting containerized environments, MeTAline can also be used on high-performance computing systems.

In simple terms, MeTAline helps researchers move from millions of confusing DNA fragments to a clearer picture of who is there, what they might be doing, and what the data could mean.

Sometimes, the biggest challenge in science isn't collecting more data — it's finding the story hidden inside it.

Read more at https://academic.oup.com/nargab/article/7/4/lqaf158/8340158?login=false

Uncovering Evolution’s Blueprint: How ntSynt Is Changing Comparative Genomics

Jitendra Narayan — Mon, 19 Oct 2026 03:08:49 -0500

Over millions of years, evolution has shaped all life on Earth, leaving clues in the DNA of every organism. While different species look and act very differently, their genomes still hold signs of a shared evolutionary past. These connections show up not just in similar DNA sequences, but also in how genetic material is arranged on chromosomes. To study these patterns, scientists use a concept called synteny, which helps them track changes in genomes, chromosome rearrangements, and relationships between species. However, as genome sequencing technology has advanced and thousands of high-quality genomes are now available, finding conserved regions across many genomes has become a much tougher computational challenge.

To tackle this problem, researchers developed a new bioinformatics tool called ntSynt. It was first introduced in a 2025 study in BMC Biology titled “ntSynt: multi-genome synteny detection using minimizer graph mappings”. This tool (https://github.com/BirolLab/ntSynt) helps researcher find conserved genomic regions across several species without relying on traditional whole-genome alignments or gene annotations. Instead, ntSynt uses short DNA sequences called minimizers as landmarks. It finds minimizers shared by different genomes and maps their relationships in a graph, making it possible to spot large genomic regions that have kept a similar structure over time. The tool uses Bloom filters and graph-based mapping, which lets scientists analyze many genomes at once while saving memory and processing time.

The team tested ntSynt using both simulated data and real genomic sequences from groups like humans, chimpanzees, bonobos, gorillas, rodents, and bees. Their results showed that ntSynt can find conserved genomic regions and spot structural differences between species. In simulated tests, ntSynt identified syntenic blocks with over 97% accuracy. One standout example involved eleven bee genomes from the genus Andrena, which have a lot of variation in chromosome organization. Despite these differences, ntSynt found conserved regions covering about 85% of the smallest bee genome, completing the analysis in just 14.7 minutes and using less than 4 GB of memory. These findings highlight ntSynt’s potential for large-scale comparative genomics, where efficiency is crucial as more genomes become available.

An interesting result came up when the researchers compared primate genomes. When they looked at regions conserved between humans and other great apes, ntSynt flagged what looked like a large deletion in one gorilla genome assembly. After checking with long-read sequencing data, they found that the missing section was likely a mistake in the assembly, not a real evolutionary change. This means ntSynt can help not only with studying evolutionary relationships but also with spotting possible errors in genome assemblies. By highlighting unexpected breaks in regions that are usually conserved, the tool helps scientists tell apart true evolutionary changes from technical mistakes in reference sequences.

The importance of ntSynt becomes even clearer when we look at global projects to sequence and study Earth’s biodiversity. Projects like the Earth BioGenome Project aim to create genomic resources for many different organisms, opening up new ways to explore the history of life. But generating genomic data is just the beginning; making sense of these relationships requires powerful and scalable tools. ntSynt helps by letting researchers study chromosome evolution, conserved genome structures, and rearrangements across many species. While the tool has some limits, especially with detecting duplicated regions or analyzing very different genomes, its speed and scalability make it a valuable tool for modern comparative genomics.

The creation of ntSynt marks a significant advancement in our understanding of how genomes have evolved and become diverse over Earth's history. Since each conserved region in the genome is evidence of common ancestry and each rearrangement gives hinThe development of ntSynt is a big step forward in understanding how genomes have changed and diversified over time. Each conserved region in a genome points to shared ancestry, and each rearrangement offers clues about evolutionary events in different lineages. ntSynt helps scientists spot these patterns more easily, opening up new ways to study genome evolution across the tree of life. Evolution’s story isn’t just in the DNA sequence, but also in how those sequences are arranged and preserved over millions of years. Tools like ntSynt are helping scientists read this hidden story more clearly and reveal the deep genomic connections that link all life on Earth.

More at https://link.springer.com/article/10.1186/s12915-025-02455-w?

TelomereHunter

Jit — Fri, 02 Feb 2018 04:23:59 -0600

TelomereHunter is a tool for estimating telomere content from human whole-genome sequencing data. It is designed to take BAM files from a tumor and a matching control sample as input. However, it is also possible to run TelomereHunter with one input file. TelomereHunter extracts and sorts telomeric reads from the input sample(s). For the estimation of telomere content, GC biases are taken into account. Finally, the results of TelomereHunter are visualized in several diagrams.

TelomereHunter is available for download at the following address: https://pypi.python.org/pypi/telomerehunter/

Address of the bookmark: http://www.dkfz.de/en/applied-bioinformatics/telomerehunter/telomerehunter.html

RAMI: a tool for identification and characterization of phylogenetic clusters in microbial communities

Jit — Mon, 07 Aug 2017 18:49:27 -0500

RAMI, which clusters related nodes in a phylogenetic tree based on the patristic distance. RAMI also produces indices of cluster properties and other indices used in population and community studies on-the-fly.

Availability: RAMI is licensed under GNU GPL and can be run or downloaded from http://www.acgt.se/online.html.

Address of the bookmark: https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btp051

ACANA: An accurate and consistent alignment tool for DNA sequences

Jit — Wed, 06 Dec 2017 09:45:29 -0600

ACANA is an accurate and consistent alignment tool for DNA sequences. ACANA is specifically designed for aligning sequences that share only some moderately conserved regions and/or have a high frequency of long insertions or deletions. It attempts to combine the best of local and global alignments algorithms in searching for evolutionarily related regions of sequences in order to achieve the best alignment. ACANA is also robust to the small changes of alignment parameters, particularly the gap extension score. As an accurate alignment tool, ACANA is particularly useful in comparative sequence analysis for identifying conserved functional regulatory elements.

Address of the bookmark: https://www.niehs.nih.gov/research/resources/software/biostatistics/acana/index.cfm

SMASH: An alignment-free tool to find and visualise rearrangements between pairs of DNA sequences

Jit — Thu, 21 Dec 2017 08:26:57 -0600

SMASH is a completely alignment-free method to find and visualise rearrangements between pairs of DNA sequences. The detection is based on relative compression, namely using a FCM, also known as Markov model, of high context order (typically 20). The method has been approached with a tool (also called SMASH). For visualization, SMASH outputs a SVG image, with an ideogram output architecture, where the patterns are represented with several HSV values (only value varies). The following image, illustrating the information maps between human and chimpanzee for the several chromosomes, depicts an example:

Address of the bookmark: https://github.com/pratas/smash

Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data

Jit — Thu, 19 Apr 2018 08:06:03 -0500

Heap, that enables robustly sensitive and accurate calling of SNPs, particularly with a low coverage NGS data, which must be aligned to the reference genome sequences in advance. To reduce false positive SNPs, Heap determines genotypes and calls SNPs at each site except for sites at the both end of reads or containing a minor allele supported by only one read. Performance comparison with existing tools showed that Heap achieved the highest F-scores with low coverage (7X) restriction-site associated DNA sequencing reads of sorghum and rice individuals. This will facilitate cost-effective GWAS and GP studies in this NGS era. Code and documentation of Heap are freely available from https://github.com/meiji-bioinf/heap and our web site (http://bioinf.mind.meiji.ac.jp/lab/en/tools.html).

Address of the bookmark: https://github.com/meiji-bioinf/heap