title: Illumina NovaSeq 6000 paired end sequencing
design: This is a negative PCR control sample where we add ddH20 as template for the PCR. For amplicon library preparation we use a two-step PCR approach. In the first step (PCR 1) we amplify the target gene: 418 base pairs of the  mitochondrial cytochrome oxidase 1 (CO1). In the second step (PCR 2) we add the indexes to the amplified sequences and fill up Illumina adapters. Detailed protocol can be found at https://doi.org/10.1371/journal.pone.0286272
library_name: P27360_1376
library_construction_protocol: CO1 was amplified using FAVIS protocol (https://doi.org/10.1371/journal.pone.0286272).  This is a negative PCR control sample where we add ddH20 as template for the amplification of the target COI fragment via PCR. For amplicon library preparation we use a two-step PCR approach. In the first step (PCR 1) we amplify the target gene: 418 base pairs of the  mitochondrial cytochrome oxidase 1 (CO1) using ddH20 as a template. After amplification, PCR products were cleaned using a ratio of 1/2.0 (v/v) of PCR product to magnetic beads. Purified PCR products were then used as template in the second round of PCR (PCR II), where sample-specific tags are added and Illumina adapters completed. The concentration of PCR II products was assessed based on the band brightness on an agarose gel. All samples were pooled approximately equimolarly to form the sequencing pool which was purified with Promega ProNexï¿½ Size-Selective Purification System, using 1/1.5 (v/v) pool to magnetic beads ratio. Samples were sequenced on NovaSeq6000 (NovaSeq Control Software 1.8.0/RTA v3.4.4) with a 251nt(Read1)-10nt(Index1)-10nt(Index2)-251nt(Read2) setup using 'NovaSeqXp' workflow in 'SP' mode flowcell. The Bcl to FastQ conversion was performed using bcl2fastq v2.20.0.422 from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+. Sequencing and demultiplexing was performed at the National Genomic Infrastructure (NGI), SciLifeLab, Stockholm, Sweden. Detailed protocol library preparation can be found at https://doi.org/10.1371/journal.pone.0286272