Gap-Centered Local Assembly: Gap Filling in Genome Drafts with Linked Reads
碩士 === 國立臺灣大學 === 生醫電子與資訊學研究所 === 107 === De novo assembly of short reads that accompanies with scaffolding algorithm often produces lots of gaps due to a lack of information to determine the sequences between contigs which leads to an incomplete draft of genomes. Here, we present a protocol for fil...
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| Other Authors: | |
| Format: | Others |
| Language: | en_US |
| Published: |
2019
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| Online Access: | http://ndltd.ncl.edu.tw/handle/ujfcbz |
| Summary: | 碩士 === 國立臺灣大學 === 生醫電子與資訊學研究所 === 107 === De novo assembly of short reads that accompanies with scaffolding algorithm often produces lots of gaps due to a lack of information to determine the sequences between contigs which leads to an incomplete draft of genomes. Here, we present a protocol for filling the gaps in genome that utilizes linked-read information contained in barcoded short reads. We validate our protocol with Japanese eel genome and show how the gaps can be filled using 10x Chromium linked reads with our local assembly methods. We expect this gap-filling protocol can be utilized for reaching more complete and high-quality scaffolds in genome assembly drafts.
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