WGS of P. waltl larvae
Libraries for Illumina sequencing were generated and sequenced at SciLifeLabs (Stockholm). Two Illumina TruSeq PCR-free libraries (insert size 180 bp) were prepared and paired end 2x125 bp sequencing was done on HiSeq2500 (HiSeq Control Software 2.2.58/RTA 1.18.64) with a setup in RapidHighOutput mode. Illumina Paired End (IPE) reads, from genomic DNA and RNA libraries, were quality filtered using the nesoni clip suit (https://github.com/Victorian-Bioinformatics-Consortium/nesoni.git). Sequencing adaptors, read bases with a per-base Phred quality value below 20 and reads shorter than 64 nucleotides were excluded. In the case that one of the two paired ends passed the quality filtered but not the counterpart, the read was kept and designated as an Illumina single end (ISE). Filtered IPE reads were merged with FLASH and these merged pairs were treated as single end reads (ISE).