The FoldX Suite builds on the strong fundament of advanced protein design features, already implemented in the successful FoldX3, and exploits the power of fragment libraries, by integrating in silico digested backbone protein fragments of different lengths. Such fragment-based strategy allows for new powerful capabilities: loop reconstruction, implemented in LoopX and peptide docking, implemented in PepX. The Suite also features an improved usability, thanks to a new boost Command Line Interface.

NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a “correct-then-assemble” strategy similar to canu (no correction step for PacBio HiFi reads), but requires significantly less computing resources and storages. After assembly, the per-base accuracy is about 98-99.8%, to further improve single base accuracy, try NextPolish.

IgCaller is a python program designed to fully characterize the immunoglobulin gene rearrangements and oncogenic translocations in lymphoid neoplasms. It was originally developed to work with WGS data but it has been extended to work with WES and high-coverage, capture-based NGS data.

MUMmer is a system for rapidly aligning entire genomes. The current version (release 4.x) can find all 20 base pair maximal exact matches between two bacterial genomes of ~5 million base pairs each in 20 seconds, using 90 MB of memory, on a typical 1.8 GHz Linux desktop computer.

Learn about SeqKit, a powerful command-line toolkit designed for handling high-throughput sequencing data with ease and efficiency.

IgBLAST is a tool commonly used in bioinformatics. IgBLAST (Immunoglobulin BLAST) is designed for the analysis of immunoglobulin (IG) and T cell receptor (TCR) sequences. It's part of the suite of tools offered by the National Center for Biotechnology Information (NCBI).

CD-HIT was originally a protein clustering program. The main advantage of this program is its ultra-fast speed. It can be hundreds of times faster than other clustering programs, for example, BLASTCLUST. Therefore it can handle very large databases, like NR. The 1st version of this program, CD-HI, was published and released in 2001. The 2nd version, called CD-HIT, was published in 2002 with significant improvements. Since 2004, CD-HIT has been hosted at bioinformatics.org as an open source project. Current CD-HIT package can perform various jobs like clustering a protein database, clustering a DNA/RNA database, comparing two databases (protein or DNA/RNA), generating protein families, and many others.

IdTrackerAI is an automated tracking software that uses deep learning algorithms to track individual animals in videos, even in challenging conditions such as occlusions and interactions between animals. The software can be used to extract a variety of metrics, including animal trajectories, activity levels, and social behavior, making it a useful tool for behavioral research in fields such as ecology, neuroscience, and psychology. Who sad this?

Cellpose is a deep learning-based software that automates cell segmentation and classification from fluorescence microscopy images. It provides a user-friendly interface and can process a large number of images in a short time, making it a valuable tool for biologists and biomedical researchers studying cell morphology and behavior. Who sad this?

Unmapped reads Annotations

DNA Seq Pipelines and tricks

This post would show you a pipeline to find the new or abnormal transcript isoforms after de-novo by Trinity

An Integrated Package for Bisulfite DNA Methylation Data Analysis with Indel-sensitive Mapping.

An Integrated Package for Bisulfite DNA Methylation Data Analysis with Indel-sensitive Mapping.

Entrez Direct: E-utilities on the UNIX Command Line