Literature DB >> 27320129

A comparison of tools for the simulation of genomic next-generation sequencing data.

Merly Escalona1, Sara Rocha1, David Posada1,2.   

Abstract

Computer simulation of genomic data has become increasingly popular for assessing and validating biological models or for gaining an understanding of specific data sets. Several computational tools for the simulation of next-generation sequencing (NGS) data have been developed in recent years, which could be used to compare existing and new NGS analytical pipelines. Here we review 23 of these tools, highlighting their distinct functionality, requirements and potential applications. We also provide a decision tree for the informed selection of an appropriate NGS simulation tool for the specific question at hand.

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Year:  2016        PMID: 27320129      PMCID: PMC5224698          DOI: 10.1038/nrg.2016.57

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  65 in total

1.  pIRS: Profile-based Illumina pair-end reads simulator.

Authors:  Xuesong Hu; Jianying Yuan; Yujian Shi; Jianliang Lu; Binghang Liu; Zhenyu Li; Yanxiang Chen; Desheng Mu; Hao Zhang; Nan Li; Zhen Yue; Fan Bai; Heng Li; Wei Fan
Journal:  Bioinformatics       Date:  2012-04-15       Impact factor: 6.937

Review 2.  High-throughput DNA sequencing--concepts and limitations.

Authors:  Martin Kircher; Janet Kelso
Journal:  Bioessays       Date:  2010-06       Impact factor: 4.345

3.  SOAP2: an improved ultrafast tool for short read alignment.

Authors:  Ruiqiang Li; Chang Yu; Yingrui Li; Tak-Wah Lam; Siu-Ming Yiu; Karsten Kristiansen; Jun Wang
Journal:  Bioinformatics       Date:  2009-06-03       Impact factor: 6.937

4.  BayesCall: A model-based base-calling algorithm for high-throughput short-read sequencing.

Authors:  Wei-Chun Kao; Kristian Stevens; Yun S Song
Journal:  Genome Res       Date:  2009-08-06       Impact factor: 9.043

Review 5.  The role of replicates for error mitigation in next-generation sequencing.

Authors:  Kimberly Robasky; Nathan E Lewis; George M Church
Journal:  Nat Rev Genet       Date:  2013-12-10       Impact factor: 53.242

6.  PBSIM: PacBio reads simulator--toward accurate genome assembly.

Authors:  Yukiteru Ono; Kiyoshi Asai; Michiaki Hamada
Journal:  Bioinformatics       Date:  2012-11-04       Impact factor: 6.937

7.  Estimation of sequencing error rates in short reads.

Authors:  Xin Victoria Wang; Natalie Blades; Jie Ding; Razvan Sultana; Giovanni Parmigiani
Journal:  BMC Bioinformatics       Date:  2012-07-30       Impact factor: 3.169

8.  Substantial biases in ultra-short read data sets from high-throughput DNA sequencing.

Authors:  Juliane C Dohm; Claudio Lottaz; Tatiana Borodina; Heinz Himmelbauer
Journal:  Nucleic Acids Res       Date:  2008-07-26       Impact factor: 16.971

9.  MetaSim: a sequencing simulator for genomics and metagenomics.

Authors:  Daniel C Richter; Felix Ott; Alexander F Auch; Ramona Schmid; Daniel H Huson
Journal:  PLoS One       Date:  2008-10-08       Impact factor: 3.240

10.  LoRDEC: accurate and efficient long read error correction.

Authors:  Leena Salmela; Eric Rivals
Journal:  Bioinformatics       Date:  2014-08-26       Impact factor: 6.937

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  46 in total

1.  Transcriptomic analysis to affirm the regulatory role of long non-coding RNA in horn cancer of Indian zebu cattle breed Kankrej (Bos indicus).

Authors:  Pritesh H Sabara; Subhash J Jakhesara; Ketankumar J Panchal; Chaitanya G Joshi; Prakash G Koringa
Journal:  Funct Integr Genomics       Date:  2019-07-31       Impact factor: 3.410

Review 2.  Reference standards for next-generation sequencing.

Authors:  Simon A Hardwick; Ira W Deveson; Tim R Mercer
Journal:  Nat Rev Genet       Date:  2017-06-19       Impact factor: 53.242

3.  Genetic Simulation Resources and the GSR Certification Program.

Authors:  Bo Peng; Man Chong Leong; Huann-Sheng Chen; Melissa Rotunno; Katy R Brignole; John Clarke; Leah E Mechanic
Journal:  Bioinformatics       Date:  2019-02-15       Impact factor: 6.937

Review 4.  Sequencing XMET genes to promote genotype-guided risk assessment and precision medicine.

Authors:  Yaqiong Jin; Geng Chen; Wenming Xiao; Huixiao Hong; Joshua Xu; Yongli Guo; Wenzhong Xiao; Tieliu Shi; Leming Shi; Weida Tong; Baitang Ning
Journal:  Sci China Life Sci       Date:  2019-05-20       Impact factor: 6.038

Review 5.  A broad survey of DNA sequence data simulation tools.

Authors:  Shatha Alosaimi; Armand Bandiang; Noelle van Biljon; Denis Awany; Prisca K Thami; Milaine S S Tchamga; Anmol Kiran; Olfa Messaoud; Radia Ismaeel Mohammed Hassan; Jacquiline Mugo; Azza Ahmed; Christian D Bope; Imane Allali; Gaston K Mazandu; Nicola J Mulder; Emile R Chimusa
Journal:  Brief Funct Genomics       Date:  2020-01-22       Impact factor: 4.241

6.  Exploring the effect of library preparation on RNA sequencing experiments.

Authors:  Lei Wang; Sara J Felts; Virginia P Van Keulen; Larry R Pease; Yuji Zhang
Journal:  Genomics       Date:  2018-12-06       Impact factor: 5.736

7.  NanoSim: nanopore sequence read simulator based on statistical characterization.

Authors:  Chen Yang; Justin Chu; René L Warren; Inanç Birol
Journal:  Gigascience       Date:  2017-04-01       Impact factor: 6.524

Review 8.  Genome sequence assembly algorithms and misassembly identification methods.

Authors:  Yue Meng; Yu Lei; Jianlong Gao; Yuxuan Liu; Enze Ma; Yunhong Ding; Yixin Bian; Hongquan Zu; Yucui Dong; Xiao Zhu
Journal:  Mol Biol Rep       Date:  2022-09-23       Impact factor: 2.742

9.  A multi-scenario genome-wide medical population genetics simulation framework.

Authors:  Jacquiline W Mugo; Ephifania Geza; Joel Defo; Samar S M Elsheikh; Gaston K Mazandu; Nicola J Mulder; Emile R Chimusa
Journal:  Bioinformatics       Date:  2017-10-01       Impact factor: 6.937

10.  GeneBreaker: Variant simulation to improve the diagnosis of Mendelian rare genetic diseases.

Authors:  Phillip A Richmond; Tamar V Av-Shalom; Oriol Fornes; Bhavi Modi; Alison M Elliott; Wyeth W Wasserman
Journal:  Hum Mutat       Date:  2021-02-10       Impact factor: 4.878

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