Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences
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DOI：
10.1093/bioinformatics/btw152
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发表时间：
2016-07-15
期刊：
影响因子：
5.8
通讯作者：
Li, Heng
中科院分区：
文献类型：
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作者：
Li, Heng
动机：单分子实时（SMRT）测序技术和牛津纳米孔技术（ONT）可产生长度超过10kb的读段，这使得以可承受的成本进行高质量的基因组组装成为可能。然而，目前长读段的错误率高达10 - 15%。组装此类读段需要复杂且计算密集型的流程。
结果：我们提出了一种新的映射工具minimap和一种从头组装工具miniasm，用于在无纠错阶段的情况下高效地映射和组装SMRT和ONT读段。它们通常能在几分钟内将一次细菌数据的测序运行组装成一个单一的重叠群，并且能在9分钟内组装45倍的秀丽隐杆线虫数据，比现有流程快几个数量级，尽管一致性序列错误率与原始读段一样高。我们还引入了一种成对读段映射格式和一种图形片段组装格式，并展示了我们的工具与现有工具之间的互操作性。
可用性和实现：https://github.com/lh3/minimap和https://github.com/lh3/miniasm
Motivation: Single Molecule Real-Time (SMRT) sequencing technology and Oxford Nanopore technologies (ONT) produce reads over 10 kb in length, which have enabled high-quality genome assembly at an affordable cost. However, at present, long reads have an error rate as high as 10-15%. Complex and computationally intensive pipelines are required to assemble such reads. Results: We present a new mapper, minimap and a de novo assembler, miniasm, for efficiently mapping and assembling SMRT and ONT reads without an error correction stage. They can often assemble a sequencing run of bacterial data into a single contig in a few minutes, and assemble 45-fold Caenorhabditis elegans data in 9 min, orders of magnitude faster than the existing pipelines, though the consensus sequence error rate is as high as raw reads. We also introduce a pairwise read mapping format and a graphical fragment assembly format, and demonstrate the interoperability between ours and current tools. Availability and implementation: https://github.com/lh3/minimap and https://github.com/lh3/miniasm