Perl script for the extraction of the most abundant sequences for each OTU and each sample

This ZIP file contains a script called GOMS: Get OTU Main Sequence. GOMS is a Perl program based on mothur files. It thus requiers several files from mothur (http://www.mothur.org/wiki/454_SOP or http://www.mothur.org/wiki/MiSeq_SOP): .list file, .names file, .groups file and .fasta file. The user m...

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Bibliographic Details
Main Authors: Galan, Maxime, Razzauti, Maria, Bard, Emilie, Bernard, Maria, Brouat, Carine, Charbonnel, Nathalie, Dehne-Garcia, Alexandre, Loiseau, Anne, Tatard, Caroline, Tamisier, Lucie, Vayssier-Taussat, Muriel, Vignes, Hélène, Cosson, Jean-François
Format: Dataset
Language:unknown
Published: Dryad Digital Repository 2016
Subjects:
Zoonoses
Rodents
West Africa
metagenomics
16S rRNA amplicon sequencing
MiSeq
Next-generation sequencing
NGS
High-throughput sequencing
HTS
Metabarcoding
Epidemiology
Disease monitoring
Senegal
Mus musculus domesticus
Rattus rattus
Mastomys natalensis
Mastomys erythroleucus
Borrelia
Bartonella
Mycoplasma
Ehrlichia
Rickettsia
Streptobacillus
Orientia
Online Access:https://dx.doi.org/10.5061/dryad.m3p7d/13
http://datadryad.org/resource/doi:10.5061/dryad.m3p7d/13
Description
Summary:This ZIP file contains a script called GOMS: Get OTU Main Sequence. GOMS is a Perl program based on mothur files. It thus requiers several files from mothur (http://www.mothur.org/wiki/454_SOP or http://www.mothur.org/wiki/MiSeq_SOP): .list file, .names file, .groups file and .fasta file. The user must also provide the number of the OTU and the treshold used to form the OTUs. GOMS generates a fasta file with, for each sample, the highly representative sequence of a given OTU, meaning the unique sequence which has the most important number of copies. Some information are also provided within the fasta file like the number of sequences and unique sequences assigned to the OTU and the number of copies of the main unique sequence.

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