Ion 318tm chip

Transcriptome sequencing was achieved using the Ion Torrent Personal Genome Machine TM (PGM) and the Ion 318 TM chip, according to the manufacturer's recommendations (Life Technologies). A total of three replicate sequencing runs were performed and the raw reads were merged into a single FASTQ file; short reads (<50 nt) were removed and the remaining sequences were trimmed at both 5 and 3 ends with the FastX-Toolkit (http://hannonlab.cshl. edu/fastx toolkit/index.html). Quality checking of the sequences was done with the FastQC tool through the RNA-Rocket platform (Warren et al., 2015) (link).
De novo assembly of the clean reads was generated with the MIRA 4.0 assembler (Chevreux et al., 2004 ). The T. trichiura transcriptome short reads dataset is publicly accessible through the European Nucleotide Archive (ENA), under accession PRJEB12315. The de novo assembled transcripts are available as a Supplementary material (Supplementary file S1).
Trimmed reads were also mapped against the recently released draft genome sequence of T. trichiura v2.1 (Foth et al., 2014) using the Ion Torrent mapper (TMAP) strategy and the CLC Genomics Workbench. Then, we associated the locus tags with their respective gene products according to T. trichiura gene annotation v. 2.2 (Foth et al., 2014) .