Artificially Generated Data Sets for Testing DNA Sequence Assembly Algorithms

Overview

Journal Genomics

Specialty Genetics

Date 1993 Apr 1

PMID 8486376

Citations 8

Authors

M L Engle

C BURKS

Affiliations

Soon will be listed here.

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.

Citing Articles

An Algorithm for Gene Fragment Reconstruction.

Fang N, Wang K, Tong D Interdiscip Sci. 2021; 13(1):118-127.

PMID: 33609237 PMC: 7896547. DOI: 10.1007/s12539-021-00419-6.

A broad survey of DNA sequence data simulation tools.

Alosaimi S, Bandiang A, van Biljon N, Awany D, Thami P, Tchamga M Brief Funct Genomics. 2019; 19(1):49-59.

PMID: 31867604 PMC: 7030445. DOI: 10.1093/bfgp/elz033.

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

Olson N, Lund S, Colman R, Foster J, Sahl J, Schupp J Front Genet. 2015; 6:235.

PMID: 26217378 PMC: 4493402. DOI: 10.3389/fgene.2015.00235.

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

Shcherbina A BMC Res Notes. 2014; 7:533.

PMID: 25123167 PMC: 4246604. DOI: 10.1186/1756-0500-7-533.

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

Pattnaik S, Gupta S, Rao A, Panda B BMC Bioinformatics. 2014; 15:40.

PMID: 24495296 PMC: 3926339. DOI: 10.1186/1471-2105-15-40.