This zenodo dataset contains raw sequencing data (Illumina total RNA-seq, Illumina differential RNA-seq, Illumina genomic DNA, Nanopore high molecular weight genomic DNA) of the polyclad flatworm Theama mediterranea. This data was used to de-novo assemble a draft genome (Flye assembler), a de-novo transcriptome (Trinity assembler), a positional tail-specific differential RNA-seq dataset (DESeq2), and a genome guided gene prediction (braker2). 1) RNA-seq (Illumina PE150) Theama_Transcriptome_1_S76_L007_R1_001.fastq.gz Theama_Transcriptome_1_S76_L007_R2_001.fastq.gz Theama_Transcriptome_2_S77_L007_R1_001.fastq.gz Theama_Transcriptome_2_S77_L007_R2_001.fastq.gz Theama_Transcriptome_3_S78_L007_R1_001.fastq.gz Theama_Transcriptome_3_S78_L007_R2_001.fastq.gz Theama_Transcriptome_4_S79_L007_R1_001.fastq.gz Theama_Transcriptome_4_S79_L007_R2_001.fastq.gz 2) Transcriptome >>> Theama_mediterranea_20200402.fasta_annotated_shortHeaders.fa (=transcriptome) TrinityStats.txt 3) diff-RNA-seq 'head' 4884-S1_S1_L005_R1_001.fastq.gz 4884-S2_S2_L005_R1_001.fastq.gz 4884-S3_S3_L005_R1_001.fastq.gz 'tail' 4884-S4_S4_L005_R1_001.fastq.gz 4884-S5_S5_L005_R1_001.fastq.gz 4884-S6_S6_L005_R1_001.fastq.gz cdhit-est 0.95 identity "transcriptome" Theama_mediterranea_20200402.fasta_annotated_shortHeaders_CDHIT95.fa Theama_mediterranea_20200402.fasta_annotated_shortHeaders_CDHIT95.fa.clstr 'head quantification' 4884-S1_S1_L005_R1_001.fastq.gz.quant.sf 4884-S2_S2_L005_R1_001.fastq.gz.quant.sf 4884-S3_S3_L005_R1_001.fastq.gz.quant.sf 'tail quantification' 4884-S4_S4_L005_R1_001.fastq.gz.quant.sf 4884-S5_S5_L005_R1_001.fastq.gz.quant.sf 4884-S6_S6_L005_R1_001.fastq.gz.quant.sf 'DESeq2' Assay_Tail_Vs_Head_clean.csv R_session 'transcripts on genomic contigs" Transcripts_on_genomic_contigs.ods 'primer list' Theama_primerlist.xlsx 4) Genomic DNA Illumina reads Theama_gDNA_illumina_1_R1.fastq.gz Theama_gDNA_illumina_1_R1.fastq.gz 5) Final polished draft genome 'unmasked polished genome' Theama_guppy5015_SUP_q7_flye283_4000ovl_medaka_1_pilon_round4_purgehaplo+mito.fasta 'repeat-masking' genome-families.fa genome-families.fa >>> Theama_guppy5015_SUP_q7_flye283_4000ovl_medaka_1_pilon_round4_purgehaplo+mito.masked (=genome) 5) Augustus gene prediction augustus.hints.aa augustus.hints.codingseq augustus.hints.gff3