The sole purpose of writing this review is
- to gain insights into the steps involved in Human Genome Assembly using either Denovo, reference guided or hybrid approach.
- Try to understand & communicate the appropriateness of either of the methods in different scenarios, their shortcomings and benefits etc.
- Seiving out the state-of-the-art assemblers/pipelines for our own benchmarking study.
- Discussing the progress and challenges still pending in the field of human genome assembly.
- Developing a step by step protocol, discussing each steps in greater detail, for each type of assembly while trying to establish the Best Practices for human genome assembly.
- Special section on mitochondrial genome assembly and methodology involved
- Discussing about assembly annotation and challenges
- Get educated on what steps must we perform benchmarking and what steps should we use the results from existing literature.
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Abstract
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Introduction
- Basics of Human Genome Assembly and various sequencing technologies, their advantages, disadvantages, assembly approaches, briefing algorithms, short highlight on mitochondrial genome assembly, and scope of the review
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De-novo assembly: Basics, algorithms
- Steps involved, factor affecting De-novo assembly
- Case studies
- Short read and long read genome assembly
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Hybrid Approach
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Steps involved, factor affecting
- Case studies
- Short read and long read genome assembly
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Mitochondrial Genome Assembly:
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Steps involved, factor affecting
- Case studies
- Short read and long read genome assembly
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Assembly Evaluation: Evaluation Statistics and tools used.
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Gap Filling for complete assembly: Algorithms and best practices
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Assembly polishing
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Assembly reconcilation merge multiple assemblies with the intent of producing a higher quality consensus assembly
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Assembly Annotation Annotating genes, TE, ncRNA
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Standards for Benchmarking: Which data to use? whether we should use simulated reads? Studies on computational necessaties for Human Genome Assembly/ mammalian genome assembly.
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Benefits of Private Cohort Derived Reference Genome: Studies and their outcome