ZOOM! Zillions of Oligos Mapped

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2008 Aug 8

PMID 18684737

Citations 78

Authors

Hao Lin

Zefeng Zhang

Michael Q Zhang

Bin Ma

Ming Li

Affiliations

Soon will be listed here.

Abstract

Motivation: The next generation sequencing technologies are generating billions of short reads daily. Resequencing and personalized medicine need much faster software to map these deep sequencing reads to a reference genome, to identify SNPs or rare transcripts.

Results: We present a framework for how full sensitivity mapping can be done in the most efficient way, via spaced seeds. Using the framework, we have developed software called ZOOM, which is able to map the Illumina/Solexa reads of 15x coverage of a human genome to the reference human genome in one CPU-day, allowing two mismatches, at full sensitivity.

Availability: ZOOM is freely available to non-commercial users at http://www.bioinfor.com/zoom

Citing Articles

Single-cell omics: experimental workflow, data analyses and applications.

Sun F, Li H, Sun D, Fu S, Gu L, Shao X Sci China Life Sci. 2024; 68(1):5-102.

PMID: 39060615 DOI: 10.1007/s11427-023-2561-0.

PerFSeeB: designing long high-weight single spaced seeds for full sensitivity alignment with a given number of mismatches.

Titarenko V, Titarenko S BMC Bioinformatics. 2023; 24(1):396.

PMID: 37875804 PMC: 10594774. DOI: 10.1186/s12859-023-05517-4.

BLEND: a fast, memory-efficient and accurate mechanism to find fuzzy seed matches in genome analysis.

Firtina C, Park J, Alser M, Kim J, Cali D, Shahroodi T NAR Genom Bioinform. 2023; 5(1):lqad004.

PMID: 36685727 PMC: 9853099. DOI: 10.1093/nargab/lqad004.

Performance optimization in DNA short-read alignment.

Wilton R, Szalay A Bioinformatics. 2022; 38(8):2081-2087.

PMID: 35139149 PMC: 10060706. DOI: 10.1093/bioinformatics/btac066.

Technology dictates algorithms: recent developments in read alignment.

Alser M, Rotman J, Deshpande D, Taraszka K, Shi H, Baykal P Genome Biol. 2021; 22(1):249.

PMID: 34446078 PMC: 8390189. DOI: 10.1186/s13059-021-02443-7.

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