FermiKit: assembly-based variant calling for Illumina resequencing data
FermiKit: assembly-based variant calling for Illumina resequencing data
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DOI：
10.1093/bioinformatics/btv440
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发表时间：
2015-11-15
期刊：
影响因子：
5.8
通讯作者：
Li, Heng
中科院分区：
文献类型：
--
作者：
Li, Heng
FermiKit是Illumina全基因组生殖系数据的变体调用管道。它从头开始组装短读段，然后根据参考基因组绘制组装图，以称为snp，短插入/缺失和结构变异。FermiKit在一台16核服务器上组装30倍的人类全基因组数据，最高内存为85 GB，并在半小时内调用变异，其精度与目前的做法相当。FermiKit组装是原始数据的简化表示，同时保留了大部分原始信息。
FermiKit is a variant calling pipeline for Illumina whole-genome germline data. It de novo assembles short reads and then maps the assembly against a reference genome to call SNPs, short insertions/deletions and structural variations. FermiKit takes about one day to assemble 30-fold human whole-genome data on a modern 16-core server with 85 GB RAM at the peak, and calls variants in half an hour to an accuracy comparable to the current practice. FermiKit assembly is a reduced representation of raw data while retaining most of the original information.