Nanopre and PacBio based Genome Assembly

Hi-C experiments explore the 3D structure of the genome, generating terabases of data to create high-resolution contact maps. Here, we introduce Juicer, an open-source tool for analyzing terabase-scale Hi-C datasets. Juicer allows users without a computational background to transform raw sequence data into normalized contact maps with one click. Juicer produces a hic file containing compressed contact matrices at many resolutions, facilitating visualization and analysis at multiple scales. Structural features, such as loops and domains, are automatically annotated.

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.

Whole Genome Sequencing (WGS) provides a deep insight into the DNA sequence of humans, animals, plants, and microbial genomes, with data analysis at the individual or population level. SNP/INDEL/CNV/SV and other variants of the genome can be fully analysed. Our sequencing analysis enables the identif wication of somatic and germline mutations as well as customized patterns of cancers and other diseases. (Novogene)

Simulated Annealing (SA) is a probabilistic technique used for finding an approximate solution to an optimization problem. It is particularly useful for problems where the search space is large and complex, and other methods might get stuck in local optima.

AI Tools for Protein Structures

The avian immune system exhibits a unique immunoglobulin (Ig) system characterized by distinct features absent in other vertebrates. Birds possess a specialized IgY, which serves as the functional equivalent to mammalian IgG and IgE, but with significant structural and functional differences. Unlike mammalian systems, birds utilize a limited number of germline gene segments and rely on gene conversion within the bursa of Fabricius to generate antibody diversity. This mechanism allows for a rapid and diverse immune response, showcasing the evolutionary adaptation of birds to their ecological niches and pathogen challenges.

The 12/23 rule is fundamental in the V(D)J recombination process, which assembles the variable (V), diversity (D), and joining (J) gene segments in the immune system to create diverse antibodies and T cell receptors. The rule stipulates that recombination can only occur between a gene segment flanked by a recombination signal sequence (RSS) with a 12-base pair (bp) spacer and one with a 23-bp spacer. This ensures proper alignment and prevents inappropriate recombination, thereby maintaining the integrity and functionality of the immune response​.

Multi-layer Neural Nets

Hidden Markov Model

Basic Mathematics Calculating

Perceptron

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