This study provides access to pre-processed reads where overlapping raw reads from the study PRJEB8682 were merged into a single longer read using the SeqPrep program. No further quality control or assembly has been performed at this stage. Quality controlled processed reads, length filtered and low quality trimmed, are available from the EBI Metagenomics resource at https://www.ebi.ac.uk/metagenomics/projects/ERP009703.