whole-genome sequencing and assembly with high-throughput, short-read technologies全基因组测序和组装与高通量、短内容的技术.pdfVIP

Whole-Genome Sequencing and Assembly with High- Throughput, Short-Read Technologies 1 2 3 4 1 Andreas Sundquist *, Mostafa Ronaghi , Haixu Tang , Pavel Pevzner , Serafim Batzoglou 1 Department of Computer Science, Stanford University, Stanford, California, United States of America, 2 Stanford Genome Technology Center, Stanford, California, United States of America, 3 School of Informatics, Indiana University, Bloomington, Indiana, United States of America, 4 Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, United States of America While recently developed short-read sequencing technologies may dramatically reduce the sequencing cost and eventually achieve the $1000 goal for re-sequencing, their limitations prevent the de novo sequencing of eukaryotic genomes with the standard shotgun sequencing protocol. We present SHRAP (SHort Read Assembly Protocol), a sequencing protocol and assembly methodology that utilizes high-throughput short-read technologies. We describe a variation on hierarchical sequencing with two crucial differences: (1) we select a clone library from the genome randomly rather than as a tiling path and (2) we sample clones from the genome at high coverage and reads from the clones at low coverage. We assume that 200 bp read lengths with a 1% error rate and inexpensive random fragment cloning on whole mammalian genomes is feasible. Our assembly methodology is based on first ordering the clones and subsequently performing read assembly in three stages: (1) local assemblies of regions significantly smaller than a clone size, (2) clone-sized assemblies of the results of stage 1, and (3) chromosome-sized assemblies. By aggressively localizing the assem