Illumina sequencing of Garcinia kola
A barcoded library from this sample was prepared as described in Mariac et al. (2014) and then paired-end sequenced on an Illumina MiSeq (2x250 bp) at the CIRAD Genotyping Platform (Montpellier, France). Demultiplexing based on internal index was performed using the PYTHON script DEMULTADAPT (https://github.com/Maillol/demultadapt) and adapters were removed using CUTADAPT 1.8 (Martin, 2011) with the following parameters: overlap length = 7, minimum length = 35 and quality = 20. Reads with a mean quality lower than 30 were discarded using a freely available PERL script (https://github.com/SouthGreenPlatform/arcad hts/blob/master/scripts/arcad_hts_2_Filter_Fastq_On_Mean_Quality.pl). R1 and R2 reads were then paired using a PERL script (https://github.com/SouthGreenPlatform/arcad-hts/blob/master/scripts/arcad_hts_3_synchronized_paired_fastq.pl).