Extracted contigs from Pleorchis sequencing experiment

Extracted DNA from the large (sailors) and the small (passengers) cercariae were sent to SNP&SEQ Platform for library preparation and sequencing. Library preparation was performed using the SMARTer ThruPLEX DNA-seq library preparation kit (Takara Bio). One library per sample was prepared. The 2 libraries were separately loaded into each lane of the Illumina SP flow cell according to Xp workflow, allowing us to obtain distinct datasets for each library and minimize any potential cross-contamination or bias. Paired-end sequencing of the libraries was performed over 150 cycles using a SP flowcell with the NovaSeq 6000 system and v1.5 sequencing chemistry (Illumina Inc.). The sequenced reads were subsequently provided in gzip-compressed fastq-formatComputational analysis was performed on both DNA samples. Although passengers demultiplexing failed, data could be recovered by using “undetermined” reads from the flow cell lane where passengers libraries were loaded. In all cases, fastq files of forward and reverse reads were trimmed using trimmomatic with a sliding window of 5:20 and a minimum length of 50. The trimmed paired reads were error corrected using SPAdes tool. For the passengers sample, an additional run of trimmomatic was performed to remove specific illumina index sequences that would affect the assembly (AATGATACGGCGACCACCGA and its reverse compliment: TCGGTGGTCGCCGTATCATT). Assembly was performed with the SPAdes on the error corrected forward and reverse reads, leading to contigs. Sequences shorter than 500 bp were discarded.