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@@ -7,7 +7,7 @@ NextDenovo is a string graph-based *de novo* assembler for TGS long reads. It us
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NextDenovo contains two core modules: NextCorrect and NextGraph. NextCorrect can be used to correct TGS long reads with approximately 15% sequencing errors, and NextGraph can be used to construct a string graph with corrected reads. It also contains a modified version of [minimap2](https://github.com/lh3/minimap2) for adapting input and output and producing more sensitive and accurate dovetail overlaps, and some useful utilities (see [here](./doc/UTILITY.md) for more details).
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So far, we have applied NextDenovo to dozens of species with various genome sizes ranging from megabytes’ level of bacteria (~ 5 MB) or fungi (\~40 MB) to gigabytes’ level of mammals (\~3 GB) or gymnosperm plants (\~20 Gb). Especially, using Nanopore ultra-long reads, we have achieved genome assemblies of a maize with contig N50 of 66 Mb, a potato with contig N50 of 57 Mb, and a rice with contig N50 of 29 Mb, of which both the maize and potato contain large amounts of repetitive elements that hamper genome assembly with long contiguity and thus have a much more fragmented assembly versions in the public database compared to the one we achieved. In addition, the rice genome assembly contain merely 18 contigs in total, revealing complete assemblies for several chromosomes (Telomere to telomere with centromere in between). In addition, we found that NextDenovo, of the current version, might produce a small number of unexpected connection errors in the highly repetitive regions, which, however, can be easily corrected using additional Hi-C or Bionano data. We are still in a progress of optimizing NextDenovo and will continuously update it, especially in terms of assembly accuracy.
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So far, we have applied NextDenovo to dozens of species with various genome sizes ranging from megabytes’ level of bacteria (\~5 MB) or fungi (\~40 MB) to gigabytes’ level of mammals (\~3 GB) or gymnosperm plants (\~20 Gb). Especially, using Nanopore ultra-long reads, we have achieved genome assemblies of a maize with contig N50 of 66 Mb, a potato with contig N50 of 57 Mb, and a rice with contig N50 of 29 Mb, of which both the maize and potato contain large amounts of repetitive elements that hamper genome assembly with long contiguity and thus have a much more fragmented assembly versions in the public database compared to the one we achieved. In addition, the rice genome assembly contain merely 18 contigs in total, revealing complete assemblies for several chromosomes (Telomere to telomere with centromere in between). In addition, we found that NextDenovo, of the current version, might produce a small number of unexpected connection errors in the highly repetitive regions, which, however, can be easily corrected using additional Hi-C or Bionano data. We are still in a progress of optimizing NextDenovo and will continuously update it, especially in terms of assembly accuracy.
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* **REQUIREMENT**
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* [Python 2.7](https://www.python.org/download/releases/2.7/)

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