BIOTECHNO 2011: THE THIRD INTERNATIONAL CONFERENCE ON BIOINFORMATICS, BIOCOMPUTATIONAL SYSTEMS AND BIOTECHNOLOGIES

Desmond Chambers

BIOTECHNO 2011: THE THIRD INTERNATIONAL CONFERENCE ON BIOINFORMATICS, BIOCOMPUTATIONAL SYSTEMS AND BIOTECHNOLOGIES

Desmond Chambers

Computer Science

Research output: Chapter in Book or Conference Publication/Proceeding › Conference Publication › peer-review

Abstract

Although second generation sequencing technology can be used to rapidly sequence an entire genome, assembly algorithms require a high level of coverage to produce a complete genomic sequence. We describe a fuzzy k-mer approach that is capable of rapidly ordering and orientating low coverage sequence reads with a high level of accuracy. Using this approach, a draft genome of Mycoplasma genitalium, sampled at varying low levels of coverage, was accurately anchored against the genome of Mycoplasma pneumoniae. The anchored reads were assembled into scaffolds with a vastly increased N50 length and an error rate of 1.5%.

Original language	English (Ireland)
Title of host publication	De Novo Draft Genome Assembly Using Fuzzy K-mers
Number of pages	6
Publication status	Published - 1 Apr 2011

Authors (Note for portal: view the doc link for the full list of authors)

Authors
Healy, J,Chambers, D,Qian, PY,Nghiem, SV

Cite this

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abstract = "Although second generation sequencing technology can be used to rapidly sequence an entire genome, assembly algorithms require a high level of coverage to produce a complete genomic sequence. We describe a fuzzy k-mer approach that is capable of rapidly ordering and orientating low coverage sequence reads with a high level of accuracy. Using this approach, a draft genome of Mycoplasma genitalium, sampled at varying low levels of coverage, was accurately anchored against the genome of Mycoplasma pneumoniae. The anchored reads were assembled into scaffolds with a vastly increased N50 length and an error rate of 1.5\%.",

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N2 - Although second generation sequencing technology can be used to rapidly sequence an entire genome, assembly algorithms require a high level of coverage to produce a complete genomic sequence. We describe a fuzzy k-mer approach that is capable of rapidly ordering and orientating low coverage sequence reads with a high level of accuracy. Using this approach, a draft genome of Mycoplasma genitalium, sampled at varying low levels of coverage, was accurately anchored against the genome of Mycoplasma pneumoniae. The anchored reads were assembled into scaffolds with a vastly increased N50 length and an error rate of 1.5%.

AB - Although second generation sequencing technology can be used to rapidly sequence an entire genome, assembly algorithms require a high level of coverage to produce a complete genomic sequence. We describe a fuzzy k-mer approach that is capable of rapidly ordering and orientating low coverage sequence reads with a high level of accuracy. Using this approach, a draft genome of Mycoplasma genitalium, sampled at varying low levels of coverage, was accurately anchored against the genome of Mycoplasma pneumoniae. The anchored reads were assembled into scaffolds with a vastly increased N50 length and an error rate of 1.5%.

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BT - De Novo Draft Genome Assembly Using Fuzzy K-mers

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BIOTECHNO 2011: THE THIRD INTERNATIONAL CONFERENCE ON BIOINFORMATICS, BIOCOMPUTATIONAL SYSTEMS AND BIOTECHNOLOGIES

Abstract

Authors (Note for portal: view the doc link for the full list of authors)

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