"In bioinformatics, sequence assembly refers to aligning and merging fragments from a longer DNA sequence in order to reconstruct the original sequence."
The process of taking short DNA sequences produced by DNA sequencing technology and assembling them into a complete genome.
Sequencing Technologies: The different sequencing technologies available for genomic sequencing, including short-read, long-read, and hybrid sequencing.
Assembly Algorithms: The different types of assembly algorithms used in genome assembly, including de novo, reference-guided, and hybrid assembly.
Quality Control and Preprocessing: The steps involved in quality checking and preprocessing raw sequencing data before assembly, including adapter trimming, base quality trimming, and read filtering.
Genome Structure and Features: The fundamental features of a genome, including genetics, nucleotide sequence, genetic code, gene structure, and regulation.
Sequence Alignment: The different methods used for sequence alignment, including pairwise alignment, multiple sequence alignment, and global and local alignment.
Variant Calling: The different methods of identifying sequence variations, including single nucleotide polymorphisms (SNPs), insertions, and deletions.
Data Visualization and Analysis: The different tools and techniques used in data visualization and analysis, including clustering, gene expression analysis, and functional annotation.
Genomic Data Management: The different methods of managing and storing genomic data, including data compression, indexing, and retrieval.
Comparative Genomics: The study of the differences and similarities between different genomes, including their structure, function, and evolution.
Metagenomics: The study of the genomes of microbial communities, including the identification of microbial species and their interactions.
Functional Genomics: The study of the functions and interactions of genes and their products, including functional analysis and pathway analysis.
Epigenomics: The study of the modifications to the genome that do not involve changes to the underlying nucleotide sequence, including DNA methylation and histone modifications.
Systems Biology: The integration of genomic, transcriptomic, proteomic, and metabolomic data to study biological systems as a whole.
Genome Editing: The use of technologies such as CRISPR/Cas9 to modify and edit the genome, including gene knockouts and gene replacements.
Ethics and Policy Issues: The ethical and policy issues surrounding the use of genomic data, including privacy, confidentiality, and data ownership.
De novo assembly: This type of genome assembly involves assembly of a genome from scratch without using any reference genome. It is often used for organisms with no available reference genome or for making improvements to existing reference genomes.
Reference-guided assembly: In this type of genome assembly, a reference genome is used as a template to guide the assembly of the target genome. This method is useful for improving the continuity and accuracy of the genome assembly.
Hybrid assembly: A combination of both de novo and reference-guided assembly, where a short-read de novo assembly and long-read reference-guided assembly are integrated to produce a more complete and accurate genome assembly.
Transcriptome-based assembly: This type of genome assembly involves assembling a genome based on the RNA sequencing data instead of DNA sequencing data. It is particularly useful for assembling the genomes of non-model organisms.
Metagenomic assembly: In this type of genome assembly, genomic data is obtained from complex environmental samples such as soil, water, and microbiome samples. It involves assembling the genomes of multiple organisms from a mixture of DNA sequences.
Phased assembly: This type of genome assembly is used to resolve heterozygosity in diploid or polyploid genomes by separating haplotype data into two separate assemblies.
PacBio that is Long-read assembly: This type of genome assembly uses PacBio sequencing technology that produces long reads up to tens of kilobases, allowing for a more contiguous genome assembly.
Hi-C assembly: In this type of genome assembly, the genome is first fragmented and then the fragments are crosslinked using Hi-C technology. The crosslinked fragments are then sequenced, and the chromatin conformation data is used to guide the genome assembly process.
Optical mapping assembly: In this type of genome assembly, a genome map is constructed using an optical mapping technique. The map is then used to assist the assembly process, resulting in a more contiguous genome assembly.
Linked-read assembly: This type of genome assembly uses a technology that tags DNA fragments before sequencing them, allowing for haplotype phasing and increasing the contiguity of the resulting genome assembly.
"DNA sequencing technology might not be able to 'read' whole genomes in one go, but rather reads small pieces of between 20 and 30,000 bases, depending on the technology used."
"Typically, the short fragments (reads) result from shotgun sequencing genomic DNA, or gene transcript (ESTs)."
"The problem of sequence assembly can be compared to taking many copies of a book, passing each of them through a shredder with a different cutter, and piecing the text of the book back together just by looking at the shredded pieces."
"Besides the obvious difficulty of this task, there are some extra practical issues: the original may have many repeated paragraphs, and some shreds may be modified during shredding to have typos. Excerpts from another book may also be added in, and some shreds may be completely unrecognizable."
"The goal of sequence assembly is to aligning and merging fragments from a longer DNA sequence in order to reconstruct the original sequence."
"DNA sequencing technology might not be able to 'read' whole genomes in one go, but rather reads small pieces."
"The short fragments (reads) result from shotgun sequencing genomic DNA, or gene transcript (ESTs)."
"The problem of sequence assembly can be compared to taking many copies of a book, passing each of them through a shredder with a different cutter, and piecing the text of the book back together just by looking at the shredded pieces."
"Besides the obvious difficulty of this task, there are some extra practical issues: the original may have many repeated paragraphs, and some shreds may be modified during shredding to have typos."
"Excerpts from another book may also be added in."
"Some shreds may be completely unrecognizable."
"In bioinformatics, sequence assembly refers to aligning and merging fragments from a longer DNA sequence in order to reconstruct the original sequence."
"DNA sequencing technology might not be able to 'read' whole genomes in one go, but rather reads small pieces of between 20 and 30,000 bases, depending on the technology used."
"The short fragments (reads) result from shotgun sequencing genomic DNA, or gene transcript (ESTs)."
"DNA sequencing technology might not be able to 'read' whole genomes in one go, but rather reads small pieces."
"the original may have many repeated paragraphs, and some shreds may be modified during shredding to have typos."
"Excerpts from another book may also be added in."
"Some shreds may be completely unrecognizable."
"In bioinformatics, sequence assembly refers to aligning and merging fragments from a longer DNA sequence in order to reconstruct the original sequence."