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GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.  

AlfaPang constructs variation graphs, leveraging its alignment-free and reference-free approach, based solely on intrinsic sequence properties. This design allows AlfaPang's runtime and memory usage to scale linearly with the size of input...

Firecrawl is an API service that takes a URL, crawls it, and converts it into clean markdown or structured data. We crawl all accessible subpages and give you clean data for each. No sitemap required. Check out our documentation. Pst....

FANTASIA is an advanced pipeline for the automatic functional annotation of protein sequences using state-of-the-art protein language models. It integrates deep learning embeddings and in-memory similarity searches, retrieving reference vectors from...

Jaeger is a tool that utilizes homology-free machine learning to identify phage genome sequences that are hidden within metagenomes. It is capable of detecting both phages and prophages within metagenomic assemblies. The performance of the Jaeger...

dna2bit: an ultra-fast and accurate genomic distance estimation software dna2bit is a software tool developed in C++11, leveraging the capabilities of OpenMP for parallel computing and the popcount technique for efficient bit manipulation. 

2,438,386 bacterial genomes at your fingertips consistently processed & characterized, enriched with metadata, accessible via a flexible search engine. BakRep (Denglish blend of Bakterien & Repository) simplifies access to this data. It...

If you’re starting out in bioinformatics or looking to sharpen your computational biology skills, having the right learning resources makes all the difference. Here’s my curated list of 10 must-read books — from beginner-friendly introductions to...

Single Nucleotide Polymorphisms (SNPs) are the most common type of genetic variation in humans—and many other organisms. A single base change in the DNA sequence (for example, an A instead of a G) can influence everything from our eye color to...

In statistics and bioinformatics, you’ll often see results reported with p-values, FDR, and q-values (q-scores). But what do these terms mean, and how are they different? Let’s break them down with simple definitions and a step-by-step example.

Convert #GFF2BED (base) [b@hn1 DUMP]$ awk 'BEGIN {OFS = "\t"};$3=="gene"{print $1,$4-1,$5}' genomic.gff > genes.bed

In today’s era of big biology, we’re generating more data than ever before—genomes, transcriptomes, proteomes, metabolomes, microbiomes… you name it. But raw biological data doesn’t speak for itself. Making sense of it requires more than...

High-throughput sequencing has become indispensable in cell biology, enabling detailed insights into chromatin structure, gene expression, and regulatory dynamics. Yet, when faced with unexpectedly low mapping rates to the human genome,...

"I have a presentation tomorrow," they say, With hopeful eyes, like it’s all child's play. As if results bloom overnight, full-grown— Not wrangled from chaos, and error-prone.

DESeq2 is a powerful and widely-used R package that identifies differentially expressed genes (DEGs) from RNA-seq data. Whether you're comparing treated vs untreated samples, disease vs healthy conditions, or wild-type vs mutant strains, DESeq2...

In a world increasingly dependent on digital data exchange, secure and user-friendly file transfer solutions are more important than ever. Enter Magic Wormhole, a deceptively simple yet powerful tool that makes it trivial to send files and...

Comparative genomics is the art and science of comparing genomes—across species, within species, or even among individuals—to unravel evolutionary relationships, functional elements, and genetic adaptations. As sequencing technologies have...

The human gut is home to trillions of microorganisms, forming one of the most complex and dynamic microbial ecosystems known to science. The Human Intestinal Bacteria Collection (HiBC) is a pioneering initiative aimed at cataloging, preserving,...

In the world of transcriptomics, quantifying gene and transcript expression accurately and efficiently is crucial. With the explosion of RNA-Seq data, researchers have turned to fast, alignment-free tools that streamline the quantification process...

In the vast and complex world of genetics, our chromosomes are like carefully arranged bookshelves — each holding critical information that defines who we are. But what happens when those books are shuffled, inverted, or swapped? The answer lies...