What question did this study set out to answer?

To introduce and evaluate MUMmer4, an updated genome alignment system redesigned to overcome input size limitations and enhance processing speed for large modern sequence datasets.

January 26, 2018SHILAP Revista de lepidopterologíaOpen Access

MUMmer4: A fast and versatile genome alignment system

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Authors

GMGuillaume Marçais ADArthur L. Delcher APAdam M. Phillippy

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Overview

Software evaluation demonstrates scalable whole-genome alignment across large eukaryotic datasets, highlighting improved computational speed and capacity for modern genomics.

Key Points

To introduce and evaluate MUMmer4, an updated genome alignment system redesigned to overcome input size limitations and enhance processing speed for large modern sequence datasets.
Replaced the core 32-bit suffix tree data structure with a 48-bit suffix array, expanding the theoretical input size limit to 141 Tbp.
Implemented multi-threaded parallel processing for query sequences and integrated script bindings for Perl, Python, and Ruby.
Benchmarked system performance and utility using whole-genome alignment of human and chimpanzee assemblies and read-to-reference mapping tests.
Successfully performed whole-genome alignment between human and chimpanzee, identifying 98% sequence identity across 96% of genome length.
Expanded sequence capacity to a theoretical maximum of 141 Tbp while improving processing speeds via multi-core parallel execution.
Enabled rapid read-to-reference alignments, though observed lower sensitivity and accuracy relative to specialized short-read aligners.

Cite This Study

Marçais et al. (2018) studied this question.

synapsesocial.com/papers/698cd0d08e28ec31f6cfb9ee https://doi.org/10.1371/journal.pcbi.1005944

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January 26, 2018SHILAP Revista de lepidopterologíaOpen Access

MUMmer4: A fast and versatile genome alignment system

View Full Paper

Ask AI

Bookmark

Authors

GMGuillaume Marçais ADArthur L. Delcher APAdam M. Phillippy

Discussion

Member takes

Overview

Software evaluation demonstrates scalable whole-genome alignment across large eukaryotic datasets, highlighting improved computational speed and capacity for modern genomics.

Key Points

To introduce and evaluate MUMmer4, an updated genome alignment system redesigned to overcome input size limitations and enhance processing speed for large modern sequence datasets.
Replaced the core 32-bit suffix tree data structure with a 48-bit suffix array, expanding the theoretical input size limit to 141 Tbp.
Implemented multi-threaded parallel processing for query sequences and integrated script bindings for Perl, Python, and Ruby.
Benchmarked system performance and utility using whole-genome alignment of human and chimpanzee assemblies and read-to-reference mapping tests.
Successfully performed whole-genome alignment between human and chimpanzee, identifying 98% sequence identity across 96% of genome length.
Expanded sequence capacity to a theoretical maximum of 141 Tbp while improving processing speeds via multi-core parallel execution.
Enabled rapid read-to-reference alignments, though observed lower sensitivity and accuracy relative to specialized short-read aligners.

Cite This Study

Marçais et al. (2018) studied this question.

synapsesocial.com/papers/698cd0d08e28ec31f6cfb9ee https://doi.org/10.1371/journal.pcbi.1005944

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