Data from: High-throughput microsatellite genotyping in ecology: improved accuracy, efficiency, standardization and success with low-quantity and degraded DNA ...

• Main Authors: De Barba, Marta, Miquel, Christian, Lobreaux, Stephane, Quenette, Pierre Yves, Swenson, Jon E., Taberlet, Pierre
• Format: Dataset
• Language: English
• Published: Dryad 2016
• Subjects: Ursus arctos; individual identification; parentage analysis; short tandem repeat STR
• Online Access: https://dx.doi.org/10.5061/dryad.18tg7; https://datadryad.org/stash/dataset/doi:10.5061/dryad.18tg7

Microsatellite markers have played a major role in ecological, evolutionary and conservation research during the past 20 years. However, technical constrains related to the use of capillary electrophoresis and a recent technological revolution that has impacted other marker types have brought to question the continued use of microsatellites for certain applications. We present a study for improving microsatellite genotyping in ecology using high-throughput sequencing (HTS). This approach entails selection of short markers suitable for HTS, sequencing PCR-amplified microsatellites on an Illumina platform and bioinformatic treatment of the sequence data to obtain multilocus genotypes. It takes advantage of the fact that HTS gives direct access to microsatellite sequences, allowing unambiguous allele identification and enabling automation of the genotyping process through bioinformatics. In addition, the massive parallel sequencing abilities expand the information content of single experimental runs far beyond ... : Readmeobitools_scriptScripts to filter raw sequence data and perform conversion to tableR_python_scriptsR and python scripts to extract genotypes from tabular data filerawdata_scandinavia.ngsfilterngsfilter file for scandinavian rawdata analysisfiltereddata_referencesassembled and filtered fastq sequences from reference samplesrawdata_pyrenees_R1Raw fastq paired-end 1 sequences from pyrenean bear samplesrawdata_pyrenees_R2Raw fastq paired-end 2 sequences from pyrenean bear samplesrawdata_scandinavia_R1Raw fastq paired-end 1 sequences from scandinavian bear samplesrawdata_scandinavia_R2Raw fastq paired-end 2 sequences from scandinavian bear samples ...