Genome-wide haplotype counting in diatoms S. robusta and P. tricornutum - processed datasets

Datasets used for genome-wide haplotype counting in S. robusta and P. tricornutum next-generation sequencing data.

For S. robusta and P. tricornutum genome-wide haplotype counting, reliable SNPs set was first identified in ILLUMINA short-read sequencing datasets and then used for counting of the number of haplotypes in the PacBio RS II and MinION long reads. The ILLUMINA and PacBio data of S. robusta were downloaded from https://www.ebi.ac.uk/ena/browser/view/PRJEB36614 and ILLUMINA and Minion data of P. tricornutum were downloaded from https://www.ebi.ac.uk/ena/browser/view/PRJNA487263.

Reference genome assembly for S. robusta: CAICTM010000001-CAICTM010004752 (European Nucleotide Archive) and

Reference genome assembly for P. tricornutum: GCA_000150955.2 (European Nucleotide Archive).

Uploaded files: 

-.bam files containing S. robusta PacBio self-corrected CCS reads aligned to reference and processed and P. tricornutum self-corrected MinION reads aligned to reference and processed:  

S_robusta_aligned_corrected_PacBio_reads.bam

P_tricornutum_aligned_corrected_MinION_reads.bam

-.table files with selected reliable SNPs used for haplotype counting with CHROM, POSITION, REFERENCE and ALTERNATIVE allele 

S_robusta_SNPs.table

P_tricornutum_SNPs.table