Literature DB >> 8486376

Artificially generated data sets for testing DNA sequence assembly algorithms.

M L Engle1, C Burks.   

Abstract

We have developed a set of tools, genfrag, to fragment and optionally mutate a DNA sequence to generate benchmark data sets for testing DNA sequence assembly algorithms. Data parameters can be systematically and independently varied to explore the range of data--and corresponding performance of assembly tools--encountered on large-scale random, or "shot-gun," sequencing projects.

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Year:  1993        PMID： 8486376     DOI： 10.1006/geno.1993.1180

Source DB:  PubMed          Journal:  Genomics        ISSN： 0888-7543            Impact factor:   5.736


  8 in total

1.  CAP3: A DNA sequence assembly program.

Authors:  X Huang; A Madan
Journal:  Genome Res       Date:  1999-09       Impact factor: 9.043

Review 2.  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

3.  Grinder: a versatile amplicon and shotgun sequence simulator.

Authors:  Florent E Angly; Dana Willner; Forest Rohwer; Philip Hugenholtz; Gene W Tyson
Journal:  Nucleic Acids Res       Date:  2012-03-19       Impact factor: 16.971

4.  rMotifGen: random motif generator for DNA and protein sequences.

Authors:  Eric C Rouchka; C Timothy Hardin
Journal:  BMC Bioinformatics       Date:  2007-08-07       Impact factor: 3.169

5.  SInC: an accurate and fast error-model based simulator for SNPs, Indels and CNVs coupled with a read generator for short-read sequence data.

Authors:  Swetansu Pattnaik; Saurabh Gupta; Arjun A Rao; Binay Panda
Journal:  BMC Bioinformatics       Date:  2014-02-05       Impact factor: 3.169

6.  FASTQSim: platform-independent data characterization and in silico read generation for NGS datasets.

Authors:  Anna Shcherbina
Journal:  BMC Res Notes       Date:  2014-08-15

7.  An Algorithm for Gene Fragment Reconstruction.

Authors:  Ningyuan Fang; Kaifa Wang; Dali Tong
Journal:  Interdiscip Sci       Date:  2021-02-20       Impact factor: 2.233

Review 8.  Best practices for evaluating single nucleotide variant calling methods for microbial genomics.

Authors:  Nathan D Olson; Steven P Lund; Rebecca E Colman; Jeffrey T Foster; Jason W Sahl; James M Schupp; Paul Keim; Jayne B Morrow; Marc L Salit; Justin M Zook
Journal:  Front Genet       Date:  2015-07-07       Impact factor: 4.599
  8 in total

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