Alignments of C. gigas in silico sequences

• Main Authors: Lapègue, Sylvie, Heurtebise, Serge, Flahauw, Emilie, Klopp, Christophe
• Format: Report
• Language: unknown
• Published: 2014
• Subjects: Aquaculture; Invertebrates; Population Genetics - Empirical; Adaptation; Crassostrea gigas
• Online Access: http://hdl.handle.net/10255/dryad.58482; https://doi.org/10.5061/dryad.jr233/1

For the in silico SNPs, we investigated in 2009 the 6th assembly of the Crassostrea gigas EST database (http://public-contigbrowser.sigenae.org:9090/Crassostrea_gigas/index.html). The database contained results of the assembly of 55,851 public ESTs from dbEST and 417 Genbank mRNA sequences. The assembly, performed with TGICL (http://compbio.dfci.harvard.edu/tgi/software/; parameters -l 60 -p 96 -s 100000 -O '-p 75 -s 500'), produced an alignment file from which 1370 SNPs were extracted. We looked for SNPs that complied with the initial criteria: a minimum depth of seven sequences, with a minimum allele count of three, and the absence of any other SNP in the 60 bp segment flanking the analyzed SNP to the left or right. As these conditions appeared too stringent, and did not produce many SNPs, we relaxed the criteria to a minimum depth of five sequences with a minimum allele count of two, and allowed there to be a SNP within 120 bp of the SNP of interest, as long as there was only one and it was not close.