Alignment Papers We are Trying to Make Sense of

Alignment Papers We are Trying to Make Sense of

Albert Einstein -

If you can’t explain it to a six year old, you don’t understand it yourself.

Yesterday, we got hold of a six year old and explained how to do Burrows Wheeler transform and reverse to him. He seemed to have enjoyed the new game. Our next goal is to understand the algorithms of following four paper in a satisfactory manner (as suggested by the above quote). The regular commentaries will resume, only when (if) the experiment succeeds. So, please wish us luck.

1. Compressed Indexing and Local Alignment of DNA - T. W. Lam et al. Bioinformatics (2008).

2. High Throughput Short Read Alignment via Bi-directional BWT - T. W. Lam et al. IEEE Bioinfo. (2009).

3. Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly - H. Li (2013).

4. Aligning sequence reads, clone sequences and assembly contigs with BWA- MEM. arXiv:1303.3997v1 - H. Li (2013).

We are also going through Heng Li’s BWA code, and especially two files -‘bwamem.c’ written by him and ‘bwt_gen.c’ from Wong Chi Kwong.

From the BWA manual -

BWA is largely influenced by BWT-SW. It uses source codes from BWT-SW and mimics its binary file formats; BWA-SW resembles BWT-SW in several ways. The initial idea about BWT-based alignment also came from the group who developed BWT-SW. At the same time, BWA is different enough from BWT-SW. The short-read alignment algorithm bears no similarity to Smith-Waterman algorithm any more. While BWA-SW learns from BWT-SW, it introduces heuristics that can hardly be applied to the original algorithm. In all, BWA does not guarantee to find all local hits as what BWT-SW is designed to do, but it is much faster than BWT-SW on both short and long query sequences.

I started to write the first piece of codes on 24 May 2008 and got the initial stable version on 02 June 2008. During this period, I was acquainted that Professor Tak-Wah Lam, the first author of BWT-SW paper, was collaborating with Beijing Genomics Institute on SOAP2, the successor to SOAP (Short Oligonucleotide Analysis Package). SOAP2 has come out in November 2008. According to the SourceForge download page, the third BWT-based short read aligner, bowtie, was first released in August 2008. At the time of writing this manual, at least three more BWT-based short-read aligners are being implemented.

The BWA-SW algorithm is a new component of BWA. It was conceived in November 2008 and implemented ten months later.

The BWA-MEM algorithm is based on an algorithm finding super-maximal exact matches (SMEMs), which was first published with the fermi assembler paper in

  1. I first implemented the basic SMEM algorithm in the fastmap command for an experiment and then extended the basic algorithm and added the extension part in Feburary 2013 to make BWA-MEM a fully featured mapper.

Written by M. //