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US 11,081,208 B2Granted
Systems, methods, and media for de novo assembly of whole genome sequence data
Assignee10x Genomics, Inc.
InventorsDavid Jaffe, Patrick Marks, Michael Schnall-Levin, Neil Weisenfeld
Life of this patent
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Abstract
Described are computer-implemented methods, systems, and media for de novo phased diploid assembly of nucleic acid sequence data generated from a nucleic acid sample of an individual utilizing nucleic acid tags to preserve long-range sequence context for the individual such that a subset of short-read sequence data derived from a common starting sequence shares a common tag. The phased diploid assembly is achieved without alignment to a reference sequence derived from organisms other than the individual. The methods, systems, and media described are computer-resource efficient, allowing scale-up.
Claims29
A computer-implemented method of de novo genome assembly for nucleic acid sequence data generated from a nucleic acid sample of an organism, the method comprising:
- (a) generating, by one or more computers, an initial assembly based on short-read sequence data, the initial assembly comprising one or more areas of unresolved sequence ambiguity, wherein the short-read sequence data is derived from longer starting sequences from the nucleic acid sequence data and is tagged to preserve long-range sequence context for the organism such that a subset of the short-read sequence data derived from a common starting sequence share one or more common tags;
- (b) generating, by the one or more computers, a plurality of local assemblies based on the initial assembly by utilizing the one or more common tags to resolve the one or more areas of unresolved sequence ambiguity, wherein the plurality of local assemblies is generated by:
- (i) using the initial assembly as an interim reference;
- (ii) identifying edges of an unambiguous sequence;
- (iii) identifying neighboring edges sharing a number of the one or more common tags above a threshold number of common tags;
- and
- (iv) bringing together edges of the unambiguous sequence with the neighboring edges identified;
- (c) generating, by the one or more computers, a global assembly based on the plurality of local assemblies;
- (d) cleaning, by the one or more computers, the global assembly by removing sequence data inconsistent with the long-range sequence context indicated by the one or more common tags;
- and
- (e) generating, by the one or more computers, a phased genome assembly based on the global assembly by utilizing the one or more common tags to separate a phased nucleotide sequence;
- wherein the phased genome assembly is achieved without alignment to a reference sequence or any independently generated genome sequence.
9 more elements
A computer-implemented system comprising:
- a digital processing device comprising:
- at least one processor, an operating system configured to perform executable instructions, a memory, and a computer program including instructions executable by the digital processing device to create a de novo genome assembly application for nucleic acid sequence data generated from a nucleic acid sample of an organism, wherein the de novo genome assembly application is programmed to:
- (a) generate an initial assembly based on short-read sequence data, the initial assembly comprising one or more areas of unresolved sequence ambiguity, wherein the short-read sequence data is derived from longer starting sequences from the nucleic acid sequence data and is tagged to preserve long-range sequence context for the organism such that a subset of the short-read sequence data derived from a common starting sequence share one or more common tags;
- (b) generate a plurality of local assemblies based on the initial assembly by utilizing the one or more common tags to resolve the one or more areas of unresolved sequence ambiguity, wherein the plurality of local assemblies is generated by:
- (i) using the initial assembly as an interim reference;
- (ii) identifying edges of an unambiguous sequence;
- (iii) identifying neighboring edges sharing a number of the one or more common tags above a threshold number of common tags;
- and
- (iv) bringing together edges of the unambiguous sequence with the neighboring edges identified;
- (c) generate a global assembly based on the plurality of local assemblies;
- (d) clean the global assembly by removing sequence data inconsistent with the long-range sequence context indicated by the one or more common tags;
- and
- (e) generate a phased genome assembly based on the global assembly by utilizing the one or more common tags to separate a homologous phased nucleotide sequence,
- wherein the de novo genome assembly application is programmed to achieve the phased genome assembly without alignment to a reference sequence or any independently generated genome sequence.
11 more elements
Non-transitory computer-readable storage media encoded with a computer program including instructions executable by a processing device to create a de novo genome assembly application for nucleic acid sequence data generated from a nucleic acid sample of an organism, wherein the de novo genome assembly application is programmed to:
- (a) generate an initial assembly based on short-read sequence data, the initial assembly comprising one or more areas of unresolved sequence ambiguity, wherein the short-read sequence data is derived from longer starting sequences from the nucleic acid sequence data and is tagged to preserve long-range sequence context for the organism such that a subset of the short-read sequence data derived from a common starting sequence share one or more common tags;
- (b) generate a plurality of local assemblies based on the initial assembly by utilizing the one or more common tags to resolve the one or more areas of unresolved sequence ambiguity, wherein the plurality of local assemblies is generated by:
- (i) using the initial assembly as an interim reference;
- (ii) identifying edges of an unambiguous sequence;
- (iii) identifying neighboring edges sharing a number of the one or more common tags above a threshold number of common tags;
- and
- (iv) bringing together edges of the unambiguous sequence with the neighboring edges identified;
- (c) generate a global assembly based on the plurality of local assemblies;
- (d) clean the global assembly by removing sequence data inconsistent with the long-range sequence context indicated by the one or more common tags;
- and
- (e) generate a phased genome assembly based on the global assembly by utilizing the one or more common tags to separate a homologous phased nucleotide sequence,
- wherein the de novo genome assembly application is programmed to achieve the phased genome assembly without alignment to a reference sequence or any independently generated genome sequence.
9 more elements
Dependencies are inferred from the claim text.