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

Trinity RNA-seq is a de novo transcriptome assembly software that uses RNA-seq data to reconstruct transcript sequences and estimate expression levels. It allows for comprehensive analysis of gene expression and isoform diversity in non-model organisms without a reference genome. Who said this?

The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

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

Capt to merger transcripts

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

Capt to merger transcripts

fastp is a fast and efficient tool for quality control and preprocessing of high-throughput sequencing data. It can perform adapter trimming, quality filtering, and read correction in a single pass, and supports various sequencing platforms and data formats.