ANDES: Statistical tools for the ANalyses of DEep Sequencing.

BMC Research Notes
Kelvin LiBarbara A Methé

Abstract

The advancements in DNA sequencing technologies have allowed researchers to progress from the analyses of a single organism towards the deep sequencing of a sample of organisms. With sufficient sequencing depth, it is now possible to detect subtle variations between members of the same species, or between mixed species with shared biomarkers, such as the 16S rRNA gene. However, traditional sequencing analyses of samples from largely homogeneous populations are often still based on multiple sequence alignments (MSA), where each sequence is placed along a separate row and similarities between aligned bases can be followed down each column. While this visual format is intuitive for a small set of aligned sequences, the representation quickly becomes cumbersome as sequencing depths cover loci hundreds or thousands of reads deep. We have developed ANDES, a software library and a suite of applications, written in Perl and R, for the statistical ANalyses of DEep Sequencing. The fundamental data structure underlying ANDES is the position profile, which contains the nucleotide distributions for each genomic position resultant from a multiple sequence alignment (MSA). Tools include the root mean square deviation (RMSD) plot, which allows...Continue Reading

References

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Citations

Jan 24, 2014·Microbiome·Alexander V AlekseyenkoMartin J Blaser
Jan 15, 2011·Molecular and Cellular Probes·Dmitriy V VolokhovVladimir E Chizhikov
Mar 31, 2015·Journal of Virological Methods·Cynthia K Y HoRichard Molenkamp
May 21, 2015·Euro Surveillance : Bulletin Européen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin·K M StuckerJ M Musser
Mar 15, 2019·Emerging Microbes & Infections·Matthijs R A WelkersDirk Eggink
Jun 22, 2012·PloS One·UNKNOWN Jumpstart Consortium Human Microbiome Project Data Generation Working Group

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Methods Mentioned

BETA
PCR
454 Titanium sequencing

Software Mentioned

clustalw
Linux
Solexa
454
MUSCLE
AMOScmp
R
BLAST
BioPerl
BioPython

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