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Miniasm+Racon:快速准确完成三代测序数据拼装

标题:

Fast and accurate de novo genome assembly from long uncorrected reads

摘要:

The assembly of long reads from Pacific Biosciences and Oxford Nanopore Technologies typically requires resource intensive error correction and consensus generation steps to obtain high quality assemblies. We show that the error correction step can be omitted and high quality consensus sequences can be generated efficiently with a SIMD accelerated, partial order alignment based stand-alone consensus module called Racon. Based on tests with PacBio and Oxford Nanopore datasets we show that Racon coupled with Miniasm enables consensus genomes with similar or better quality than state-of-the-art methods while being an order of magnitude faster.

地址:

http://biorxiv.org/content/early/2016/08/05/068122

源码:

https://github.com/isovic/racon

安装:

git clone https://github.com/isovic/racon.git && cd racon && make modules && make tools && make -j

导读:

三代测序拼装软件,三代测序平台 Nanopore / Pacbio 产生的数据的一个共同点就是,读长长,错误率高,在用于分析之前需要对数据进行特殊处理(consensus,错误纠正),再进行拼装任务,Liheng 开发的 Miniasm 可以直接使用未处理的长读长序列进行快速拼装,但是Miniasm对拼装的Contig序列进行抛光处理,所以会出现不少SNP/INDEL, Racon 就是为了解决这个问题,支持 (GFA, FASTA, FASTQ, SAM, MHAP and PAF) 等文件输入格式,相对于 Quiver / Nanopolish 通用性更高,这样一套新的组合 Miniasm+Racon 出现了,高校快速。

版本:

2016-10-15.v1

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