计算基因组学论文阅读

论文阅读记录

日期	标题	作者	期刊/会议	源码
2022/10/31	Fast and accurate short read alignment with Burrows-Wheeler transform	Li H. and Durbin R	Bioinformatics	https://github.com/lh3/bwa
2022/11/07	Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM	Li Heng	Bioinformatics	https://github.com/lh3/bwa
2022/11/14	High Throughput Short Read Alignment via Bi-directional BWT	T.W. Lam∗, Ruiqiang Li†, Alan Tam∗, Simon Wong∗, Edward Wu∗, S.M. Yiu∗	Bioinformatics	https://github.com/lh3/bwa

论文主题

短序列（读长）比对算法（Short read alignment）

1. DNA短序列（读长）比对（DNA short-read alignment）

已读	年份	名字	题目	简介	引用
⬜	2008	MAQ	Mapping short DNA sequencing reads and calling variants using mapping quality scores	基于hash-table的DNA短读长比对算法
✅	2009	BWA	Fast and accurate short read alignment with Burrows-Wheeler transform	基于BWT的DNA短读长比对算法
⬜	2009	Bowtie	Ultrafast and memory-efficient alignment of short DNA sequences to the human genome	基于BWT的DNA短读长比对算法
✅	2009	SMEMs	High Throughput Short Read Alignment via Bi-directional BWT	基于双向BWT的高通量短读长比对算法
⬜	2012	SeqAlto	Fast and accurate read alignment for resequencing	基于hash-table的DNA短读长比对算法
⬜	2012	GEM	The GEM mapper: fast, accurate and versatile alignment by filtration	基于hash-table的DNA短读长比对算法
✅	2013	BWA-MEM	Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM	基于BWT的DNA短读长比对算法
⬜	2013	Bowtie2	Fast gapped-read alignment with Bowtie 2	基于BWT的DNA短读长比对算法