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

• 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

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.