Genomic assemblers:

Researchers and scientists always deal with the genomics data in genomics and bioinformatics. The genomic data gathered from different resources is not always in structural form. Sometimes it is very difficult to assemble the fragments and get the desired results. In this case, the technology always plays an important role in making our tasks easier and more efficient. Assembling a sequence manually is tough if the genome to large.  So, to deal with this problem, researchers use tools known as genomic Assemblers. Genomic assemblers help us to reconstruct the genetic information from the raw data easily. This article is particularly going to explain the application of genomic assemblers and some popular genomic assemblers.

Understanding Gene Assembly:

Genome sequencing follows a step of fragmentation. Extracted genome is first fragmented into pieces. Fragments of the DNA go through different procedures and the fragments and then reassembled to get the desired sequence. The reassembling of the fragments is now gene assembly.  Gene assembles are helpers for reassembling the fragments in the correct order. So overall gene assemblers play vital role in genome assembly.

Key Components of Gene Assemblers:

1.        Read Alignment:

Gene assemblers begin by aligning short DNA fragments, or reads, against a reference genome or assembling them de novo without a reference. This step is critical for identifying overlaps and similarities among the reads.

2.        Overlap Detection:

The assembler identifies regions where reads overlap, providing crucial information about the order and orientation of the fragments. This step is fundamental in constructing the larger genomic picture.

3.        Contig Formation:

Contigs are contiguous stretches of DNA sequence assembled from the overlapping reads. Gene assemblers aim to construct longer contigs, reducing fragmentation and improving the accuracy of the assembled genome.

4.        Scaffold Building:

Scaffolds are formed by connecting contigs with gaps representing regions where the sequence is not covered. This step enhances the continuity of the assembly, providing a more complete representation of the genome.

Popular Genomic Assemblers:

a.        SPAdes:

SPAdes is a widely used de novo genome assembler. SPAdes performs well on various types of sequencing data, including short and long reads.

b.        Velvet:

Velvet is known for its efficiency in handling large volumes of short-read data and has been influential in many genome projects.

c.        SOAPdenovo:

SOAPdenovo excels in assembling genomes without a reference. SOAPdenovo is suitable for large and complex genomes.

Applications of genomic assemblers

Genome Sequencing:

Gene assemblers are indispensable in the process of decoding the entire genome of an organism, providing insights into its genetic makeup.

Metagenomics:

They play a vital role in metagenomic studies, where the genetic material of entire microbial communities is sequenced and assembled.

Comparative Genomics:

By assembling genomes, researchers can compare the genetic makeup of different organisms. Unravelling evolutionary relationships and identifying unique genomic features.

Challenges and Future Directions:

Just like other technologies the genome assembler also faces significant challenges during the assembly process. The sequencing errors and repetitive sequences may affect the accuracy of the assembly process. However, the continuous advancements in algorithm development aim to address this challenge. Researchers ensure more precise and reliable genome reconstructions in the future.

Conclusion:

Gene assemblers stand at the forefront of genomic research.  It enables scientists to unlock the secrets hidden within the DNA sequences of diverse organisms. As technology evolves, so too will the capabilities of these assemblers, bringing us closer to a more comprehensive understanding of the intricate genetic codes that govern life on Earth.